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Iodine in PDB 3mce: Crystal Structure of the Nac Domain of Alpha Subunit of Nascent Polypeptide-Associated Complex(Nac)

Protein crystallography data

The structure of Crystal Structure of the Nac Domain of Alpha Subunit of Nascent Polypeptide-Associated Complex(Nac), PDB code: 3mce was solved by L.F.Wang, W.C.Zhang, L.Wang, X.J.C.Zhang, X.M.Li, Z.Rao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.90 / 2.40
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 54.592, 59.605, 69.130, 90.00, 90.00, 90.00
R / Rfree (%) 24.7 / 27.7

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of the Nac Domain of Alpha Subunit of Nascent Polypeptide-Associated Complex(Nac) (pdb code 3mce). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 8 binding sites of Iodine where determined in the Crystal Structure of the Nac Domain of Alpha Subunit of Nascent Polypeptide-Associated Complex(Nac), PDB code: 3mce:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iodine binding site 1 out of 8 in 3mce

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Iodine binding site 1 out of 8 in the Crystal Structure of the Nac Domain of Alpha Subunit of Nascent Polypeptide-Associated Complex(Nac)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of the Nac Domain of Alpha Subunit of Nascent Polypeptide-Associated Complex(Nac) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I3

b:18.3
occ:0.35
 O A:HOH23 3.3 51.4 1.0
C A:SER77 3.5 73.0 1.0
N A:PRO78 3.6 56.7 1.0
N A:GLY73 3.6 56.6 1.0
N A:SER77 3.7 35.4 1.0
CA A:SER77 3.8 30.0 1.0
O A:SER77 3.8 39.2 1.0
CD A:PRO78 4.0 31.1 1.0
CA A:PRO78 4.1 39.4 1.0
NZ A:LYS82 4.2 34.1 1.0
C A:GLY76 4.2 56.2 1.0
CG A:PRO78 4.2 59.6 1.0
CE A:LYS82 4.4 30.7 1.0
O C:HOH16 4.5 44.6 1.0
O A:GLY76 4.6 35.8 1.0
CB A:PRO78 4.7 31.7 1.0
O A:HOH5 4.8 40.9 1.0
O A:GLY73 4.8 58.3 1.0
O A:HOH6 4.9 30.8 1.0
CA A:GLY73 4.9 35.2 1.0

Iodine binding site 2 out of 8 in 3mce

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Iodine binding site 2 out of 8 in the Crystal Structure of the Nac Domain of Alpha Subunit of Nascent Polypeptide-Associated Complex(Nac)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of the Nac Domain of Alpha Subunit of Nascent Polypeptide-Associated Complex(Nac) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I7

b:19.9
occ:0.17
 CA A:GLY90 3.6 56.1 1.0
CE B:LYS98 4.0 58.4 1.0
N A:GLY90 4.1 57.5 1.0
CG B:LYS98 4.1 50.5 1.0
CB B:SER99 4.4 47.4 1.0
CD B:LYS98 4.5 54.8 1.0
CG2 A:THR89 4.7 70.1 1.0
C A:GLY90 4.8 56.5 1.0
C A:THR89 4.9 62.0 1.0

Iodine binding site 3 out of 8 in 3mce

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Iodine binding site 3 out of 8 in the Crystal Structure of the Nac Domain of Alpha Subunit of Nascent Polypeptide-Associated Complex(Nac)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structure of the Nac Domain of Alpha Subunit of Nascent Polypeptide-Associated Complex(Nac) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I1

b:20.5
occ:0.81
 CG B:ARG93 3.3 43.6 1.0
OG1 B:THR95 3.4 39.0 1.0
OG1 A:THR95 3.5 41.6 1.0
NH2 A:ARG97 3.6 61.5 1.0
O B:ARG93 3.7 44.0 1.0
CZ A:ARG97 3.7 63.7 1.0
CB B:THR95 3.7 39.1 1.0
CB A:THR95 3.8 40.4 1.0
O B:HOH15 3.9 51.9 1.0
CB A:ARG97 3.9 56.3 1.0
NE A:ARG97 3.9 62.6 1.0
N B:THR95 3.9 40.5 1.0
O A:THR95 4.0 39.1 1.0
CD B:ARG93 4.1 43.3 1.0
CD1 A:LEU103 4.1 47.5 1.0
C B:ARG93 4.2 42.9 1.0
NH1 A:ARG97 4.2 66.1 1.0
C A:THR95 4.3 40.1 1.0
N A:ARG97 4.3 52.6 1.0
CB B:ARG93 4.4 43.1 1.0
NE B:ARG93 4.4 42.8 1.0
CA B:THR95 4.5 39.2 1.0
C B:VAL94 4.5 41.6 1.0
CA B:VAL94 4.6 41.4 1.0
CA A:THR95 4.7 40.0 1.0
N B:VAL94 4.7 41.5 1.0
CD A:ARG97 4.7 61.2 1.0
N A:ILE96 4.8 42.7 1.0
CA A:ARG97 4.8 55.8 1.0
C A:ILE96 4.9 48.2 1.0
CG2 A:THR95 4.9 41.1 1.0
CA B:ARG93 4.9 41.8 1.0
CG2 B:THR95 4.9 40.6 1.0
CG A:ARG97 4.9 58.4 1.0
CA A:ILE96 5.0 44.5 1.0

Iodine binding site 4 out of 8 in 3mce

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Iodine binding site 4 out of 8 in the Crystal Structure of the Nac Domain of Alpha Subunit of Nascent Polypeptide-Associated Complex(Nac)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystal Structure of the Nac Domain of Alpha Subunit of Nascent Polypeptide-Associated Complex(Nac) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I5

b:16.2
occ:0.26
 N B:ASN101 3.5 45.5 1.0
OG B:SER99 3.5 46.1 1.0
CB B:SER99 3.8 47.4 1.0
CB B:ASN101 3.8 44.1 1.0
ND2 B:ASN101 3.9 47.5 1.0
CD1 B:ILE102 3.9 37.4 1.0
N B:LYS100 4.0 46.9 1.0
CA B:ASN101 4.1 43.9 1.0
OG B:SER132 4.1 48.9 1.0
CG1 B:ILE102 4.3 36.7 1.0
CG B:ASN101 4.3 47.8 1.0
N B:ILE102 4.4 39.0 1.0
C B:LYS100 4.5 45.6 1.0
C B:ASN101 4.5 40.5 1.0
CA B:LYS100 4.6 46.2 1.0
CB B:LYS100 4.7 47.8 1.0
O B:LYS98 4.7 42.0 1.0
C B:SER99 4.8 47.8 1.0
CA B:SER99 4.9 47.1 1.0

Iodine binding site 5 out of 8 in 3mce

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Iodine binding site 5 out of 8 in the Crystal Structure of the Nac Domain of Alpha Subunit of Nascent Polypeptide-Associated Complex(Nac)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Crystal Structure of the Nac Domain of Alpha Subunit of Nascent Polypeptide-Associated Complex(Nac) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I6

b:18.8
occ:0.12
 OG1 A:THR95 3.0 41.6 1.0
CG2 B:THR95 3.1 40.6 1.0
O B:THR95 3.5 40.1 1.0
CG A:ARG93 3.5 44.1 1.0
CG B:ARG97 3.5 37.6 1.0
CB B:THR95 3.7 39.1 1.0
CD B:ARG97 3.8 36.8 1.0
C B:THR95 3.9 38.7 1.0
CG2 A:THR95 4.0 41.1 1.0
CD A:ARG93 4.0 46.5 1.0
CB A:THR95 4.1 40.4 1.0
O A:ARG93 4.1 42.5 1.0
N A:THR95 4.2 40.8 1.0
NE A:ARG93 4.2 48.6 1.0
CB A:ARG93 4.2 42.2 1.0
C A:ARG93 4.3 42.4 1.0
CB B:ARG97 4.3 38.4 1.0
CA A:VAL94 4.4 42.1 1.0
N B:ARG97 4.4 40.1 1.0
C A:VAL94 4.4 40.6 1.0
N A:VAL94 4.4 42.2 1.0
CA B:THR95 4.5 39.2 1.0
N B:ILE96 4.5 37.0 1.0
CA B:ILE96 4.7 38.6 1.0
C B:ILE96 4.8 38.1 1.0
CA A:THR95 4.8 40.0 1.0
OG1 B:THR95 4.9 39.0 1.0
CA A:ARG93 4.9 43.0 1.0
CA B:ARG97 5.0 40.8 1.0

Iodine binding site 6 out of 8 in 3mce

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Iodine binding site 6 out of 8 in the Crystal Structure of the Nac Domain of Alpha Subunit of Nascent Polypeptide-Associated Complex(Nac)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Crystal Structure of the Nac Domain of Alpha Subunit of Nascent Polypeptide-Associated Complex(Nac) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I4

b:39.1
occ:0.30
 CG2 C:THR95 3.1 41.4 1.0
NH1 C:ARG97 3.4 67.3 1.0
OG1 D:THR95 3.6 45.6 1.0
NE D:ARG93 4.0 66.5 1.0
CB C:THR95 4.0 39.7 1.0
CG C:ARG97 4.3 58.5 1.0
CG2 D:THR95 4.3 41.8 1.0
CG D:ARG93 4.3 54.0 1.0
O C:THR95 4.5 39.0 1.0
CB D:THR95 4.6 42.7 1.0
CD D:ARG93 4.6 59.9 1.0
CZ C:ARG97 4.7 66.3 1.0
O D:ARG93 4.7 41.7 1.0
CB C:ARG97 4.8 54.5 1.0
C C:THR95 4.8 37.4 1.0
OG1 C:THR95 4.9 40.6 1.0
NH2 D:ARG93 4.9 71.6 1.0
N D:THR95 4.9 39.1 1.0
CB D:ARG93 4.9 49.4 1.0
CZ D:ARG93 4.9 70.5 1.0
CD1 C:LEU103 4.9 51.2 1.0

Iodine binding site 7 out of 8 in 3mce

Go back to Iodine Binding Sites List in 3mce
Iodine binding site 7 out of 8 in the Crystal Structure of the Nac Domain of Alpha Subunit of Nascent Polypeptide-Associated Complex(Nac)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Crystal Structure of the Nac Domain of Alpha Subunit of Nascent Polypeptide-Associated Complex(Nac) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I8

b:9.1
occ:0.16
 N C:ASN101 3.4 69.8 1.0
N C:LYS100 3.6 75.0 1.0
CB C:SER99 3.6 74.2 1.0
CD1 C:ILE102 3.8 64.8 1.0
CB C:LYS100 4.0 77.4 1.0
CA C:LYS100 4.1 74.5 1.0
CB C:ASN101 4.2 68.5 1.0
CA C:ASN101 4.2 68.5 1.0
C C:LYS100 4.3 71.5 1.0
CG1 C:ILE102 4.4 62.2 1.0
O C:LYS98 4.5 56.6 1.0
OG C:SER99 4.5 76.3 1.0
N C:ILE102 4.5 64.1 1.0
C C:SER99 4.6 73.9 1.0
ND2 C:ASN101 4.6 68.7 1.0
C C:ASN101 4.7 66.3 1.0
CA C:SER99 4.7 71.3 1.0
CG C:ASN101 5.0 67.9 1.0

Iodine binding site 8 out of 8 in 3mce

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Iodine binding site 8 out of 8 in the Crystal Structure of the Nac Domain of Alpha Subunit of Nascent Polypeptide-Associated Complex(Nac)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Crystal Structure of the Nac Domain of Alpha Subunit of Nascent Polypeptide-Associated Complex(Nac) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:I2

b:26.9
occ:0.50
 OG1 D:THR95 3.4 45.6 1.0
OG1 C:THR95 3.7 40.6 1.0
O C:ARG93 3.8 46.4 1.0
NE D:ARG97 3.8 79.3 1.0
CG C:ARG93 3.8 44.5 1.0
O D:THR95 3.9 35.5 1.0
NE C:ARG93 4.0 48.7 1.0
CB D:THR95 4.0 42.7 1.0
CB C:THR95 4.0 39.7 1.0
CB D:ARG97 4.0 67.5 1.0
C D:THR95 4.1 38.8 1.0
CB C:ARG93 4.2 45.2 1.0
CD1 D:LEU103 4.2 47.7 1.0
C C:ARG93 4.2 45.5 1.0
N C:THR95 4.3 40.6 1.0
N D:ARG97 4.3 57.0 1.0
CD C:ARG93 4.4 47.0 1.0
N D:ILE96 4.5 40.6 1.0
CD D:ARG97 4.5 76.0 1.0
NH2 D:ARG97 4.5 82.4 1.0
CZ D:ARG97 4.7 81.9 1.0
C C:VAL94 4.7 40.8 1.0
CA D:THR95 4.7 40.4 1.0
CA C:VAL94 4.7 38.6 1.0
CG D:ARG97 4.7 72.1 1.0
N C:VAL94 4.7 42.5 1.0
C D:ILE96 4.7 52.1 1.0
CA D:ILE96 4.8 45.2 1.0
CA D:ARG97 4.8 62.6 1.0
CA C:THR95 4.8 38.6 1.0
CZ C:ARG93 4.9 51.0 1.0
CA C:ARG93 4.9 45.6 1.0
NH2 C:ARG93 5.0 51.5 1.0

Reference:

L.F.Wang, W.C.Zhang, L.Wang, X.J.C.Zhang, X.M.Li, Z.Rao. Crystal Structures of Nac Domains of Human Nascent Polypeptide-Associated Complex (Nac) and Its Alphanac Subunit Protein Cell V. 1 406 2010.
ISSN: ISSN 1674-800X
PubMed: 21203952
DOI: 10.1007/S13238-010-0049-3
Page generated: Fri Aug 8 14:42:05 2025

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