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Iodine in PDB 2v8i: Structure of A Family 2 Pectate Lyase in A Native Form

Enzymatic activity of Structure of A Family 2 Pectate Lyase in A Native Form

All present enzymatic activity of Structure of A Family 2 Pectate Lyase in A Native Form:
4.2.2.2;

Protein crystallography data

The structure of Structure of A Family 2 Pectate Lyase in A Native Form, PDB code: 2v8i was solved by D.W.Abbott, A.B.Boraston, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.59 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 58.486, 95.642, 126.608, 90.00, 90.00, 90.00
R / Rfree (%) 22.2 / 24.3

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 51;

Binding sites:

The binding sites of Iodine atom in the Structure of A Family 2 Pectate Lyase in A Native Form (pdb code 2v8i). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 51 binding sites of Iodine where determined in the Structure of A Family 2 Pectate Lyase in A Native Form, PDB code: 2v8i:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 51 in 2v8i

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Iodine binding site 1 out of 51 in the Structure of A Family 2 Pectate Lyase in A Native Form


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Structure of A Family 2 Pectate Lyase in A Native Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1547

b:3.2
occ:1.00
 OG A:SER496 3.1 18.4 1.0
CD2 A:HIS443 3.4 26.3 1.0
CB A:SER496 3.6 17.7 1.0
O A:HOH2647 3.6 25.3 1.0
CB A:HIS443 3.9 20.1 1.0
O A:HOH2703 3.9 25.3 1.0
O A:HOH2700 3.9 21.6 1.0
CG A:HIS443 4.0 23.8 1.0
CA A:SER496 4.0 17.6 1.0
O A:HOH2301 4.3 39.1 1.0
CB A:PRO501 4.3 20.8 1.0
CD2 A:TYR442 4.3 18.7 1.0
CA A:HIS443 4.4 20.0 1.0
CE2 A:TYR442 4.5 18.7 1.0
O A:LEU439 4.5 16.6 1.0
NE2 A:HIS443 4.6 26.1 1.0
O A:HOH2635 4.7 43.1 1.0
N A:HIS443 4.9 18.3 1.0
CG A:PRO501 4.9 20.7 1.0
N A:SER496 4.9 16.7 1.0

Iodine binding site 2 out of 51 in 2v8i

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Iodine binding site 2 out of 51 in the Structure of A Family 2 Pectate Lyase in A Native Form


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Structure of A Family 2 Pectate Lyase in A Native Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1548

b:13.0
occ:0.50
 I A:IOD1597 2.2 13.0 0.5
CA A:PRO545 3.5 30.2 1.0
N A:PRO545 3.6 29.6 1.0
CD A:ARG526 3.9 18.9 1.0
C A:GLN544 3.9 28.6 1.0
CE A:MET520 3.9 29.2 1.0
CG A:ARG526 4.0 19.5 1.0
CG A:MET520 4.0 27.7 1.0
O A:GLN544 4.1 28.3 1.0
CG A:PRO545 4.1 30.2 1.0
CD A:PRO545 4.1 29.9 1.0
NE A:ARG526 4.2 18.1 1.0
CB A:PRO545 4.2 30.5 1.0
CB A:ARG526 4.4 20.8 1.0
SD A:MET520 4.4 29.7 1.0
O A:LEU543 4.7 25.0 1.0
C A:PRO545 4.7 30.8 1.0
CA A:GLN544 4.8 27.4 1.0
N A:ASN546 4.9 31.6 1.0

Iodine binding site 3 out of 51 in 2v8i

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Iodine binding site 3 out of 51 in the Structure of A Family 2 Pectate Lyase in A Native Form


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Structure of A Family 2 Pectate Lyase in A Native Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1549

b:10.8
occ:1.00
 OG A:SER123 3.0 29.5 1.0
I A:IOD1552 3.2 18.8 1.0
CB A:SER123 3.7 29.1 1.0
CE1 A:HIS109 3.7 22.2 1.0
O A:HOH2212 4.1 33.0 1.0
CG A:GLU515 4.1 19.8 1.0
OE1 A:GLU515 4.1 28.6 1.0
CA A:GLY516 4.2 17.0 1.0
O A:HOH2082 4.2 42.9 1.0
CD A:GLU515 4.3 24.7 1.0
ND1 A:HIS109 4.3 21.7 1.0
N A:GLY516 4.4 17.0 1.0
O A:GLU515 4.6 17.2 1.0
CA A:SER528 4.6 20.5 1.0
OG A:SER528 4.6 25.0 1.0
C A:GLU515 4.6 16.7 1.0
O A:HOH2726 4.6 49.1 1.0
NE2 A:HIS109 4.8 21.3 1.0
N A:SER528 4.8 20.9 1.0
CA A:SER123 4.8 28.7 1.0
CB A:GLU515 4.9 17.0 1.0
CG A:GLU126 4.9 25.3 1.0
O A:HOH2222 4.9 54.9 1.0
C A:GLY516 5.0 17.8 1.0

Iodine binding site 4 out of 51 in 2v8i

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Iodine binding site 4 out of 51 in the Structure of A Family 2 Pectate Lyase in A Native Form


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Structure of A Family 2 Pectate Lyase in A Native Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1550

b:12.1
occ:1.00
 O A:HOH2747 3.2 23.3 1.0
N A:GLN544 3.6 26.1 1.0
NH2 A:ARG526 3.8 18.9 1.0
CD2 A:LEU543 4.1 20.3 1.0
O A:HOH2329 4.1 27.0 1.0
CA A:LEU543 4.2 23.2 1.0
O A:HOH2330 4.3 35.4 1.0
OE2 A:GLU533 4.3 21.3 1.0
CB A:GLN544 4.4 27.6 1.0
O A:HOH2746 4.4 34.5 1.0
C A:LEU543 4.4 24.3 1.0
O A:HOH2758 4.4 49.9 1.0
O A:HOH2754 4.5 56.5 1.0
CA A:GLN544 4.5 27.4 1.0
O A:GLN544 4.6 28.3 1.0
CG A:GLN544 4.6 29.1 1.0
CZ A:ARG526 4.8 18.5 1.0
CB A:LEU543 4.8 23.0 1.0
CD2 A:LEU537 4.8 18.5 1.0
CB A:GLU533 4.8 15.5 1.0
CD A:GLU533 4.9 18.0 1.0
O A:LYS542 4.9 21.2 1.0

Iodine binding site 5 out of 51 in 2v8i

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Iodine binding site 5 out of 51 in the Structure of A Family 2 Pectate Lyase in A Native Form


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Structure of A Family 2 Pectate Lyase in A Native Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1551

b:12.6
occ:1.00
 O A:HOH2599 2.9 49.7 1.0
O A:HOH2626 3.3 59.3 1.0
N A:SER430 3.5 17.9 1.0
O A:HOH2628 3.6 39.4 1.0
OG A:SER430 3.9 18.8 1.0
NH2 A:ARG465 4.0 18.4 1.0
N A:ASP431 4.0 16.4 1.0
CA A:ASN429 4.1 19.3 1.0
OD1 A:ASN429 4.2 23.1 1.0
CG A:ASN429 4.2 21.2 1.0
C A:ASN429 4.3 18.5 1.0
CA A:SER430 4.3 17.4 1.0
O A:HOH2630 4.3 39.0 1.0
C A:SER430 4.3 17.1 1.0
CB A:ASP431 4.4 16.0 1.0
ND2 A:ASN429 4.4 20.7 1.0
CA A:ASP431 4.6 16.1 1.0
CB A:SER430 4.7 17.8 1.0
CB A:ASN429 4.8 19.4 1.0
O A:THR428 4.8 21.3 1.0

Iodine binding site 6 out of 51 in 2v8i

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Iodine binding site 6 out of 51 in the Structure of A Family 2 Pectate Lyase in A Native Form


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Structure of A Family 2 Pectate Lyase in A Native Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1552

b:18.8
occ:1.00
 O A:HOH2726 2.5 49.1 1.0
I A:IOD1549 3.2 10.8 1.0
I A:IOD1576 3.3 29.3 1.0
N A:SER528 3.4 20.9 1.0
N A:ALA517 3.6 18.5 1.0
O A:HOH2212 3.7 33.0 1.0
C A:GLY516 3.7 17.8 1.0
CA A:GLY516 3.9 17.0 1.0
OG A:SER123 4.0 29.5 1.0
CB A:VAL527 4.0 21.3 1.0
CA A:VAL527 4.1 20.9 1.0
O A:GLY516 4.2 17.8 1.0
CA A:SER528 4.2 20.5 1.0
CA A:ALA517 4.2 19.4 1.0
C A:VAL527 4.2 20.5 1.0
CB A:ALA517 4.3 19.9 1.0
OG A:SER528 4.4 25.0 1.0
CG1 A:VAL527 4.5 22.3 1.0
CB A:SER123 4.5 29.1 1.0
CA A:SER123 4.7 28.7 1.0
O A:HOH2082 4.8 42.9 1.0
N A:GLY516 4.9 17.0 1.0
CB A:SER528 5.0 21.2 1.0

Iodine binding site 7 out of 51 in 2v8i

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Iodine binding site 7 out of 51 in the Structure of A Family 2 Pectate Lyase in A Native Form


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Structure of A Family 2 Pectate Lyase in A Native Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1553

b:17.1
occ:1.00
 NZ A:LYS368 3.2 20.5 1.0
O A:HOH2560 3.3 32.4 1.0
O A:HOH2085 3.4 30.9 1.0
CE A:LYS368 3.9 21.0 1.0
O A:HOH2219 4.4 40.7 1.0
CD A:LYS368 4.5 18.9 1.0
I A:IOD1578 4.6 20.4 1.0

Iodine binding site 8 out of 51 in 2v8i

Go back to Iodine Binding Sites List in 2v8i
Iodine binding site 8 out of 51 in the Structure of A Family 2 Pectate Lyase in A Native Form


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Structure of A Family 2 Pectate Lyase in A Native Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1554

b:16.5
occ:1.00
 O A:HOH2290 2.6 40.6 1.0
O A:HOH2315 2.7 51.6 1.0
O A:HOH2729 3.1 37.8 1.0
N A:LEU543 3.4 21.9 1.0
CG A:LEU543 3.9 22.2 1.0
CB A:LYS542 3.9 21.8 1.0
CA A:LYS542 4.0 21.8 1.0
CB A:LEU543 4.0 23.0 1.0
CD1 A:LEU543 4.1 20.7 1.0
C A:LYS542 4.2 21.6 1.0
CA A:LEU543 4.3 23.2 1.0
CE2 A:TYR518 4.4 23.8 1.0
CG A:LYS542 4.5 22.9 1.0
CE A:MET520 4.5 29.2 1.0
OH A:TYR518 4.6 22.7 1.0
SD A:MET520 4.6 29.7 1.0
O A:HOH2731 4.7 45.6 1.0
CD A:LYS542 4.8 23.6 1.0
CD1 A:LEU537 4.8 18.1 1.0
CZ A:TYR518 4.9 22.3 1.0

Iodine binding site 9 out of 51 in 2v8i

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Iodine binding site 9 out of 51 in the Structure of A Family 2 Pectate Lyase in A Native Form


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Structure of A Family 2 Pectate Lyase in A Native Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1555

b:19.5
occ:1.00
 O A:HOH2357 2.2 54.3 1.0
N A:LEU199 2.7 21.8 1.0
CB A:LEU199 3.0 23.2 1.0
O A:HOH2354 3.3 41.3 1.0
CA A:LEU199 3.3 22.5 1.0
O A:LEU199 3.4 22.7 1.0
CG A:LEU199 3.5 24.4 1.0
C A:GLY198 3.8 20.9 1.0
OG A:SER170 3.8 20.4 1.0
CD1 A:LEU199 3.8 26.1 1.0
C A:LEU199 3.8 22.0 1.0
CA A:GLY198 4.0 20.1 1.0
CA A:SER170 4.0 19.0 1.0
N A:ARG171 4.0 18.1 1.0
CB A:SER170 4.1 19.3 1.0
NE A:ARG171 4.3 31.2 1.0
CG A:ARG171 4.3 21.8 1.0
CD A:ARG171 4.4 26.2 1.0
C A:SER170 4.6 18.6 1.0
O A:THR169 4.6 19.5 1.0
O A:LYS197 4.6 19.0 1.0
O A:GLY198 4.9 21.4 1.0
CD2 A:LEU199 4.9 24.3 1.0
CB A:ARG171 5.0 18.4 1.0

Iodine binding site 10 out of 51 in 2v8i

Go back to Iodine Binding Sites List in 2v8i
Iodine binding site 10 out of 51 in the Structure of A Family 2 Pectate Lyase in A Native Form


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Structure of A Family 2 Pectate Lyase in A Native Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1556

b:16.5
occ:1.00
 O A:HOH2652 2.6 40.2 1.0
NE A:ARG451 3.4 17.7 1.0
NH2 A:ARG451 3.7 19.9 1.0
CZ A:ARG451 4.0 18.9 1.0
CG A:LYS452 4.1 21.0 1.0
O A:ALA448 4.1 19.1 1.0
CB A:ARG451 4.2 15.8 1.0
OE2 A:GLU455 4.2 25.4 1.0
CG A:ARG451 4.4 15.4 1.0
CB A:ALA448 4.4 19.6 1.0
CD A:ARG451 4.5 16.5 1.0
N A:LYS452 4.6 17.3 1.0
CA A:ALA448 4.6 18.7 1.0
C A:ALA448 4.8 19.1 1.0
C A:ARG451 4.9 17.1 1.0
CD A:LYS452 5.0 22.0 1.0
CD A:GLU455 5.0 22.6 1.0
CD2 A:LEU497 5.0 19.0 1.0

Reference:

D.W.Abbott, A.B.Boraston. A Family 2 Pectate Lyase Displays A Rare Fold and Transition Metal-Assisted -Elimination. J.Biol.Chem. V. 282 35328 2007.
ISSN: ISSN 0021-9258
PubMed: 17881361
DOI: 10.1074/JBC.M705511200
Page generated: Sun Aug 11 14:24:01 2024

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