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Zinc in PDB 2o6p: Crystal Structure of the Heme-Isdc Complex

Protein crystallography data

The structure of Crystal Structure of the Heme-Isdc Complex, PDB code: 2o6p was solved by K.H.Sharp, S.Schneider, A.Cockayne, M.Paoli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.99 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 47.489, 70.441, 88.685, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 22.2

Other elements in 2o6p:

The structure of Crystal Structure of the Heme-Isdc Complex also contains other interesting chemical elements:

Iron (Fe) 2 atoms
Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Heme-Isdc Complex (pdb code 2o6p). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of the Heme-Isdc Complex, PDB code: 2o6p:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 2o6p

Go back to Zinc Binding Sites List in 2o6p
Zinc binding site 1 out of 6 in the Crystal Structure of the Heme-Isdc Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Heme-Isdc Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1004

b:22.1
occ:0.75
O1A B:HEM190 2.1 32.1 1.0
O A:HOH1053 2.1 28.3 1.0
O A:HOH1065 2.2 20.3 1.0
ND1 A:HIS134 2.2 20.1 1.0
CGA B:HEM190 2.9 29.4 1.0
O2A B:HEM190 2.9 32.9 1.0
CE1 A:HIS134 3.2 20.1 1.0
CG A:HIS134 3.3 18.9 1.0
CB A:HIS134 3.6 17.9 1.0
CMA B:HEM190 3.8 20.7 1.0
CA A:HIS134 3.8 17.3 1.0
N A:HIS135 4.0 17.2 1.0
O A:HIS135 4.3 17.5 1.0
C3A B:HEM190 4.3 19.6 1.0
CBA B:HEM190 4.3 27.0 1.0
NE2 A:HIS134 4.3 18.9 1.0
CD2 A:HIS134 4.4 18.1 1.0
O A:ASP133 4.5 17.6 1.0
C A:HIS134 4.5 17.8 1.0
CD1 B:ILE48 4.5 18.5 0.5
O A:HOH1074 4.5 39.1 1.0
C2A B:HEM190 4.6 20.6 1.0
CAA B:HEM190 4.7 22.4 1.0
CE1 A:TYR136 5.0 15.8 1.0
N A:HIS134 5.0 16.9 1.0
CD1 B:ILE48 5.0 17.4 0.5
C A:HIS135 5.0 17.3 1.0

Zinc binding site 2 out of 6 in 2o6p

Go back to Zinc Binding Sites List in 2o6p
Zinc binding site 2 out of 6 in the Crystal Structure of the Heme-Isdc Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Heme-Isdc Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1006

b:40.4
occ:0.75
NE2 A:HIS135 2.1 24.9 0.8
OD1 A:ASP133 2.1 20.6 1.0
O A:HOH1083 2.2 51.8 1.0
CE1 A:HIS135 2.9 24.7 0.8
CG A:ASP133 3.0 18.4 1.0
OD2 A:ASP133 3.2 20.1 1.0
CD2 A:HIS135 3.2 24.1 0.8
O A:HOH1084 3.3 28.3 1.0
O A:HOH1082 3.8 50.1 1.0
ND1 A:HIS135 4.1 24.7 0.8
CG A:HIS135 4.3 21.8 0.8
O A:HOH1085 4.4 30.0 1.0
CB A:ASP133 4.4 17.4 1.0
C A:ASP133 4.5 17.1 1.0
O A:ASP133 4.5 17.6 1.0
N A:HIS134 4.7 16.9 1.0
CA A:ASP133 4.8 17.0 1.0

Zinc binding site 3 out of 6 in 2o6p

Go back to Zinc Binding Sites List in 2o6p
Zinc binding site 3 out of 6 in the Crystal Structure of the Heme-Isdc Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Heme-Isdc Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1001

b:18.5
occ:1.00
OD1 B:ASP133 2.0 18.5 1.0
NE2 B:HIS135 2.0 18.0 1.0
CG B:ASP133 2.8 18.2 1.0
OD2 B:ASP133 3.0 19.2 1.0
CD2 B:HIS135 3.0 16.6 1.0
CE1 B:HIS135 3.0 17.4 1.0
O B:HOH1009 3.7 19.4 1.0
ND1 B:HIS135 4.1 16.2 1.0
CG B:HIS135 4.2 16.1 1.0
CB B:ASP133 4.3 18.4 1.0
O B:HOH1017 4.3 24.3 1.0
C B:ASP133 4.4 17.3 1.0
O B:ASP133 4.4 17.5 1.0
N B:HIS134 4.7 16.7 1.0
O B:HOH1026 4.8 30.0 1.0
CA B:ASP133 4.8 17.8 1.0

Zinc binding site 4 out of 6 in 2o6p

Go back to Zinc Binding Sites List in 2o6p
Zinc binding site 4 out of 6 in the Crystal Structure of the Heme-Isdc Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Heme-Isdc Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1003

b:23.9
occ:0.75
NE2 B:HIS134 2.0 21.8 1.0
O1A A:HEM190 2.0 27.1 1.0
O B:HOH1051 2.3 31.2 1.0
O B:HOH1103 2.3 21.6 1.0
CGA A:HEM190 2.9 25.7 1.0
CE1 B:HIS134 3.0 22.5 1.0
CD2 B:HIS134 3.0 20.0 1.0
O2A A:HEM190 3.1 27.8 1.0
O A:HOH1059 4.1 39.7 1.0
ND1 B:HIS134 4.1 20.7 1.0
CG B:HIS134 4.1 18.7 1.0
CD1 B:TYR132 4.2 17.6 1.0
CBA A:HEM190 4.3 24.0 1.0
CE1 B:TYR132 4.4 17.9 1.0
N B:ASP133 4.7 17.8 1.0
CAA A:HEM190 4.8 21.5 1.0
CA B:TYR132 4.8 19.9 1.0
CG B:TYR132 4.9 18.5 1.0
O B:ASP133 5.0 17.5 1.0

Zinc binding site 5 out of 6 in 2o6p

Go back to Zinc Binding Sites List in 2o6p
Zinc binding site 5 out of 6 in the Crystal Structure of the Heme-Isdc Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the Heme-Isdc Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1002

b:17.7
occ:1.00
O B:GLY28 2.2 16.9 1.0
N B:GLY28 2.2 17.4 1.0
C B:GLY28 2.9 17.3 1.0
CA B:GLY28 2.9 17.5 1.0
N B:SER29 4.2 17.8 1.0
CA B:SER29 5.0 18.5 1.0

Zinc binding site 6 out of 6 in 2o6p

Go back to Zinc Binding Sites List in 2o6p
Zinc binding site 6 out of 6 in the Crystal Structure of the Heme-Isdc Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the Heme-Isdc Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1005

b:21.3
occ:0.75
O B:HOH1088 2.0 21.0 1.0
NZ B:LYS58 2.0 23.3 1.0
O B:HOH1098 2.4 15.5 0.5
O B:HOH1098 2.9 14.0 0.5
CE B:LYS58 3.0 23.3 1.0
O B:HOH1076 4.1 23.8 1.0
OG B:SER31 4.1 18.8 1.0
O B:HOH1099 4.3 24.0 0.5
CD B:LYS58 4.3 22.5 1.0
O B:HOH1099 4.6 31.1 0.5
CB B:SER31 4.8 18.9 1.0
O B:HOH1102 4.9 27.5 1.0

Reference:

K.H.Sharp, S.Schneider, A.Cockayne, M.Paoli. Crystal Structure of the Heme-Isdc Complex, the Central Conduit of the Isd Iron/Heme Uptake System in Staphylococcus Aureus. J. Biol. Chem. V. 282 10625 2007.
ISSN: ISSN 0021-9258
PubMed: 17287214
DOI: 10.1074/JBC.M700234200
Page generated: Thu Oct 17 02:31:35 2024

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