Iodine in PDB 2v8i: 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;

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

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 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 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 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 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 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 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 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 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 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 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

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