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Iron in PDB 3use: Crystal Structure of E. Coli Hydrogenase-1 in Its As-Isolated Form

Enzymatic activity of Crystal Structure of E. Coli Hydrogenase-1 in Its As-Isolated Form

All present enzymatic activity of Crystal Structure of E. Coli Hydrogenase-1 in Its As-Isolated Form:
1.12.99.6;

Protein crystallography data

The structure of Crystal Structure of E. Coli Hydrogenase-1 in Its As-Isolated Form, PDB code: 3use was solved by A.Volbeda, J.C.Fontecilla-Camps, C.Darnault, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.82 / 1.67
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 93.930, 97.790, 183.290, 90.00, 90.00, 90.00
R / Rfree (%) 12 / 16.8

Other elements in 3use:

The structure of Crystal Structure of E. Coli Hydrogenase-1 in Its As-Isolated Form also contains other interesting chemical elements:

Nickel (Ni) 2 atoms
Magnesium (Mg) 2 atoms
Chlorine (Cl) 3 atoms

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 32;

Binding sites:

The binding sites of Iron atom in the Crystal Structure of E. Coli Hydrogenase-1 in Its As-Isolated Form (pdb code 3use). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 32 binding sites of Iron where determined in the Crystal Structure of E. Coli Hydrogenase-1 in Its As-Isolated Form, PDB code: 3use:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 32 in 3use

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Iron binding site 1 out of 32 in the Crystal Structure of E. Coli Hydrogenase-1 in Its As-Isolated Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of E. Coli Hydrogenase-1 in Its As-Isolated Form within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe401

b:8.0
occ:1.00
FE1 S:SF4401 0.0 8.0 1.0
S3 S:SF4401 2.3 8.3 1.0
S4 S:SF4401 2.3 8.3 1.0
SG S:CYS215 2.3 8.8 1.0
S2 S:SF4401 2.3 7.7 1.0
FE3 S:SF4401 2.7 8.7 1.0
FE2 S:SF4401 2.7 7.9 1.0
FE4 S:SF4401 2.7 8.3 1.0
CB S:CYS215 3.5 8.1 1.0
N S:LEU216 3.8 7.6 1.0
S1 S:SF4401 3.9 7.4 1.0
CA S:CYS215 3.9 6.6 1.0
N S:TYR217 4.2 8.7 1.0
C S:CYS215 4.3 8.0 1.0
CB S:PHE196 4.4 9.1 1.0
CD1 S:PHE196 4.4 10.1 1.0
ND1 S:HIS187 4.5 7.1 1.0
CB S:TYR217 4.6 8.7 1.0
CE1 S:HIS187 4.7 10.4 1.0
CB S:ARG192 4.7 7.8 1.0
O S:ARG192 4.7 8.1 1.0
CG S:PHE196 4.8 10.6 1.0
CA S:LEU216 4.8 8.6 1.0
CA S:TYR217 4.8 7.2 1.0
C S:LEU216 4.8 7.3 1.0
SG S:CYS221 4.9 8.3 1.0
SG S:CYS190 4.9 8.0 1.0

Iron binding site 2 out of 32 in 3use

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Iron binding site 2 out of 32 in the Crystal Structure of E. Coli Hydrogenase-1 in Its As-Isolated Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of E. Coli Hydrogenase-1 in Its As-Isolated Form within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe401

b:7.9
occ:1.00
FE2 S:SF4401 0.0 7.9 1.0
S4 S:SF4401 2.3 8.3 1.0
S3 S:SF4401 2.3 8.3 1.0
SG S:CYS190 2.3 8.0 1.0
S1 S:SF4401 2.3 7.4 1.0
FE3 S:SF4401 2.7 8.7 1.0
FE4 S:SF4401 2.7 8.3 1.0
FE1 S:SF4401 2.7 8.0 1.0
CB S:CYS190 3.1 6.2 1.0
S2 S:SF4401 3.9 7.7 1.0
CB S:ARG192 4.2 7.8 1.0
CD1 S:ILE243 4.2 7.8 1.0
CG2 S:ILE243 4.3 5.6 1.0
ND1 S:HIS187 4.5 7.1 1.0
CA S:CYS190 4.6 7.1 1.0
C S:ARG192 4.7 7.6 1.0
N S:ARG192 4.7 7.7 1.0
CA S:ARG192 4.7 6.7 1.0
SG S:CYS221 4.8 8.3 1.0
N S:ARG193 4.8 7.8 1.0
CG1 S:ILE243 4.8 6.6 1.0
SG S:CYS215 4.9 8.8 1.0
C S:CYS190 5.0 6.5 1.0

Iron binding site 3 out of 32 in 3use

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Iron binding site 3 out of 32 in the Crystal Structure of E. Coli Hydrogenase-1 in Its As-Isolated Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of E. Coli Hydrogenase-1 in Its As-Isolated Form within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe401

b:8.7
occ:1.00
FE3 S:SF4401 0.0 8.7 1.0
ND1 S:HIS187 2.1 7.1 1.0
S1 S:SF4401 2.3 7.4 1.0
S4 S:SF4401 2.3 8.3 1.0
S2 S:SF4401 2.3 7.7 1.0
FE2 S:SF4401 2.7 7.9 1.0
FE1 S:SF4401 2.7 8.0 1.0
FE4 S:SF4401 2.7 8.3 1.0
CE1 S:HIS187 2.8 10.4 1.0
CG S:HIS187 3.2 9.6 1.0
CB S:HIS187 3.8 7.2 1.0
S3 S:SF4401 3.9 8.3 1.0
NE2 S:HIS187 4.0 11.5 1.0
CA S:HIS187 4.0 7.8 1.0
CD2 S:HIS187 4.2 11.1 1.0
CG S:PRO224 4.2 9.7 1.0
CD S:PRO224 4.3 8.5 1.0
CB S:CYS190 4.5 6.2 1.0
SG S:CYS190 4.7 8.0 1.0
SG S:CYS215 4.7 8.8 1.0
CD1 S:PHE196 4.7 10.1 1.0
SG S:CYS221 4.8 8.3 1.0
CD S:ARG193 4.8 14.3 1.0
N S:PRO224 4.8 8.5 1.0
O S:HIS187 4.8 9.8 1.0
C S:HIS187 5.0 9.1 1.0
N S:HIS187 5.0 6.5 1.0

Iron binding site 4 out of 32 in 3use

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Iron binding site 4 out of 32 in the Crystal Structure of E. Coli Hydrogenase-1 in Its As-Isolated Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of E. Coli Hydrogenase-1 in Its As-Isolated Form within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe401

b:8.3
occ:1.00
FE4 S:SF4401 0.0 8.3 1.0
S2 S:SF4401 2.3 7.7 1.0
S1 S:SF4401 2.3 7.4 1.0
S3 S:SF4401 2.3 8.3 1.0
SG S:CYS221 2.3 8.3 1.0
FE2 S:SF4401 2.7 7.9 1.0
FE3 S:SF4401 2.7 8.7 1.0
FE1 S:SF4401 2.7 8.0 1.0
CB S:CYS221 3.2 6.3 1.0
S4 S:SF4401 3.9 8.3 1.0
CD1 S:ILE243 3.9 7.8 1.0
CG1 S:ILE243 4.4 6.6 1.0
CA S:GLY223 4.5 7.2 1.0
CD S:PRO224 4.5 8.5 1.0
N S:GLY223 4.6 6.8 1.0
ND1 S:HIS187 4.6 7.1 1.0
CA S:CYS221 4.6 6.7 1.0
SG S:CYS215 4.7 8.8 1.0
SG S:CYS190 4.7 8.0 1.0
N S:TYR217 4.8 8.7 1.0
N S:LEU216 4.8 7.6 1.0
C S:CYS221 4.9 7.5 1.0
CB S:LEU216 4.9 7.2 1.0
C S:LEU216 5.0 7.3 1.0

Iron binding site 5 out of 32 in 3use

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Iron binding site 5 out of 32 in the Crystal Structure of E. Coli Hydrogenase-1 in Its As-Isolated Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of E. Coli Hydrogenase-1 in Its As-Isolated Form within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe402

b:7.6
occ:1.00
FE1 S:F3S402 0.0 7.6 1.0
S1 S:F3S402 2.2 6.9 1.0
S2 S:F3S402 2.2 7.3 1.0
S3 S:F3S402 2.2 6.9 1.0
SG S:CYS252 2.3 7.2 1.0
FE4 S:F3S402 2.6 7.0 1.0
FE3 S:F3S402 2.7 7.2 1.0
CB S:CYS252 3.4 6.7 1.0
O L:HOH756 3.7 8.0 1.0
N S:CYS252 3.8 6.9 1.0
S4 S:F3S402 3.9 8.0 1.0
O S:HOH508 4.0 8.1 1.0
CA S:CYS252 4.0 7.5 1.0
N S:ALA253 4.5 7.3 1.0
C S:CYS252 4.5 7.3 1.0
O L:HOH740 4.5 11.1 1.0
ND2 S:ASN228 4.6 6.4 1.0
SG S:CYS230 4.7 7.1 1.0
SG S:CYS249 4.7 7.1 1.0
C S:GLY251 5.0 6.9 1.0
CG S:PRO242 5.0 5.8 1.0

Iron binding site 6 out of 32 in 3use

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Iron binding site 6 out of 32 in the Crystal Structure of E. Coli Hydrogenase-1 in Its As-Isolated Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of E. Coli Hydrogenase-1 in Its As-Isolated Form within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe402

b:7.2
occ:1.00
FE3 S:F3S402 0.0 7.2 1.0
S4 S:F3S402 2.2 8.0 1.0
S1 S:F3S402 2.2 6.9 1.0
S3 S:F3S402 2.2 6.9 1.0
SG S:CYS230 2.3 7.1 1.0
FE1 S:F3S402 2.7 7.6 1.0
FE4 S:F3S402 2.7 7.0 1.0
CB S:CYS230 3.2 5.0 1.0
S2 S:F3S402 3.9 7.3 1.0
ND2 S:ASN228 4.0 6.4 1.0
CD1 S:ILE186 4.2 8.3 1.0
O S:HOH508 4.3 8.1 1.0
NE1 S:TRP235 4.3 8.0 1.0
CG S:PRO242 4.5 5.8 1.0
CD S:PRO242 4.5 5.5 1.0
CG S:ASN228 4.6 6.4 1.0
CA S:CYS230 4.7 5.5 1.0
CB S:ASN228 4.7 6.6 1.0
SG S:CYS252 4.7 7.2 1.0
CG1 S:ILE186 4.7 9.5 1.0
SG S:CYS249 4.8 7.1 1.0

Iron binding site 7 out of 32 in 3use

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Iron binding site 7 out of 32 in the Crystal Structure of E. Coli Hydrogenase-1 in Its As-Isolated Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of E. Coli Hydrogenase-1 in Its As-Isolated Form within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe402

b:7.0
occ:1.00
FE4 S:F3S402 0.0 7.0 1.0
S4 S:F3S402 2.2 8.0 1.0
S2 S:F3S402 2.3 7.3 1.0
S3 S:F3S402 2.3 6.9 1.0
SG S:CYS249 2.3 7.1 1.0
FE1 S:F3S402 2.6 7.6 1.0
FE3 S:F3S402 2.7 7.2 1.0
CB S:CYS249 3.2 5.7 1.0
CA S:CYS249 3.6 6.5 1.0
S1 S:F3S402 3.8 6.9 1.0
N S:LEU250 4.0 6.2 1.0
N S:GLY251 4.2 6.2 1.0
C S:CYS249 4.3 6.0 1.0
N S:CYS252 4.4 6.9 1.0
CG2 S:THR226 4.6 7.1 1.0
CG1 S:ILE186 4.6 9.5 1.0
CG S:PRO242 4.7 5.8 1.0
SG S:CYS252 4.7 7.2 1.0
CA S:GLY251 4.8 7.1 1.0
SG S:CYS230 4.8 7.1 1.0
N S:CYS249 4.9 6.9 1.0
O L:HOH740 5.0 11.1 1.0
CD1 S:ILE186 5.0 8.3 1.0

Iron binding site 8 out of 32 in 3use

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Iron binding site 8 out of 32 in the Crystal Structure of E. Coli Hydrogenase-1 in Its As-Isolated Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of E. Coli Hydrogenase-1 in Its As-Isolated Form within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe403

b:10.4
occ:0.50
FE1 S:F4S403 0.0 10.4 0.5
FE4 S:SF3404 0.0 10.4 0.5
S2 S:F4S403 2.3 8.9 0.5
S3 S:SF3404 2.3 8.9 0.5
S1 S:F4S403 2.3 8.4 0.5
S2 S:SF3404 2.3 8.4 0.5
SG S:CYS17 2.3 8.4 1.0
SG S:CYS19 2.4 8.5 1.0
FE2 S:F4S403 2.6 8.8 0.5
FE1 S:SF3404 2.6 8.8 0.5
FE4 S:F4S403 2.7 10.2 0.5
FE7 S:SF3404 3.2 10.7 0.5
CB S:CYS19 3.5 7.3 1.0
CB S:CYS17 3.5 5.9 1.0
FE3 S:F4S403 3.6 8.0 0.5
FE3 S:SF3404 3.6 8.0 0.5
N S:CYS19 3.7 6.5 1.0
N S:CYS17 3.7 8.1 1.0
S3 S:F4S403 3.7 8.3 0.5
S1 S:SF3404 3.7 8.3 0.5
CA S:CYS17 4.0 6.6 1.0
N S:THR18 4.1 7.6 1.0
CA S:CYS19 4.1 7.3 1.0
NE2 L:HIS229 4.2 8.4 1.0
C S:CYS17 4.2 8.1 1.0
SG S:CYS149 4.4 6.8 1.0
O S:HOH502 4.5 7.7 1.0
SG S:CYS115 4.6 8.8 1.0
N S:CYS20 4.7 7.2 1.0
CD2 L:HIS229 4.8 7.3 1.0
C S:THR18 4.8 7.2 1.0
OE2 S:GLU76 4.9 13.0 0.5
C S:GLU16 4.9 9.2 1.0
C S:CYS19 4.9 7.1 1.0
SG S:CYS20 5.0 8.7 1.0
CG L:ARG74 5.0 5.8 1.0

Iron binding site 9 out of 32 in 3use

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Iron binding site 9 out of 32 in the Crystal Structure of E. Coli Hydrogenase-1 in Its As-Isolated Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of E. Coli Hydrogenase-1 in Its As-Isolated Form within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe403

b:8.8
occ:0.50
FE2 S:F4S403 0.0 8.8 0.5
FE1 S:SF3404 0.0 8.8 0.5
S3 S:F4S403 2.2 8.3 0.5
S1 S:SF3404 2.2 8.3 0.5
SG S:CYS115 2.3 8.8 1.0
S1 S:F4S403 2.3 8.4 0.5
S2 S:SF3404 2.3 8.4 0.5
S2 S:F4S403 2.3 8.9 0.5
S3 S:SF3404 2.3 8.9 0.5
FE1 S:F4S403 2.6 10.4 0.5
FE4 S:SF3404 2.6 10.4 0.5
FE3 S:F4S403 2.7 8.0 0.5
FE3 S:SF3404 2.7 8.0 0.5
FE4 S:F4S403 3.0 10.2 0.5
CB S:CYS115 3.3 6.4 1.0
FE7 S:SF3404 3.9 10.7 0.5
O S:HOH520 3.9 8.6 1.0
N S:CYS115 4.0 5.9 1.0
SG S:CYS19 4.1 8.5 1.0
O S:HOH502 4.2 7.7 1.0
CA S:CYS115 4.2 6.6 1.0
SG S:CYS120 4.3 8.3 1.0
CB S:CYS120 4.4 6.6 1.0
N S:CYS17 4.6 8.1 1.0
SG S:CYS20 4.6 8.7 1.0
SG S:CYS149 4.7 6.8 1.0
SG S:CYS17 4.8 8.4 1.0
CA S:GLU16 4.9 8.8 1.0
CB S:GLU16 4.9 11.6 1.0

Iron binding site 10 out of 32 in 3use

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Iron binding site 10 out of 32 in the Crystal Structure of E. Coli Hydrogenase-1 in Its As-Isolated Form


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of E. Coli Hydrogenase-1 in Its As-Isolated Form within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe403

b:8.0
occ:0.50
FE3 S:F4S403 0.0 8.0 0.5
FE3 S:SF3404 0.0 8.0 0.5
SG S:CYS149 2.3 6.8 1.0
S3 S:F4S403 2.3 8.3 0.5
S1 S:SF3404 2.3 8.3 0.5
S2 S:F4S403 2.3 8.9 0.5
S3 S:SF3404 2.3 8.9 0.5
SG S:CYS120 2.3 8.3 1.0
FE2 S:F4S403 2.7 8.8 0.5
FE1 S:SF3404 2.7 8.8 0.5
CB S:CYS149 3.3 6.7 1.0
CB S:CYS120 3.4 6.6 1.0
FE1 S:F4S403 3.6 10.4 0.5
FE4 S:SF3404 3.6 10.4 0.5
CA S:CYS149 4.0 5.7 1.0
SG S:CYS115 4.0 8.8 1.0
FE4 S:F4S403 4.2 10.2 0.5
SG S:CYS19 4.3 8.5 1.0
CG L:ARG74 4.4 5.8 1.0
N S:CYS115 4.5 5.9 1.0
CB S:THR114 4.6 6.5 1.0
S1 S:F4S403 4.7 8.4 0.5
S2 S:SF3404 4.7 8.4 0.5
CA S:CYS120 4.8 6.2 1.0
N S:VAL121 4.9 6.8 1.0
C S:CYS149 4.9 6.1 1.0
O S:GLY148 4.9 6.2 1.0
N S:THR114 5.0 6.4 1.0

Reference:

A.Volbeda, P.Amara, C.Darnault, J.M.Mouesca, A.Parkin, M.M.Roessler, F.A.Armstrong, J.C.Fontecilla-Camps. X-Ray Crystallographic and Computational Studies of the O2-Tolerant [Nife]-Hydrogenase 1 From Escherichia Coli. Proc.Natl.Acad.Sci.Usa V. 109 5305 2012.
ISSN: ISSN 0027-8424
PubMed: 22431599
DOI: 10.1073/PNAS.1119806109
Page generated: Sun Aug 4 21:17:12 2024

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