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Iron in PDB 5lmm: Structure of E Coli Hydrogenase Hyd-1 Mutant E28Q

Enzymatic activity of Structure of E Coli Hydrogenase Hyd-1 Mutant E28Q

All present enzymatic activity of Structure of E Coli Hydrogenase Hyd-1 Mutant E28Q:
1.12.99.6;

Protein crystallography data

The structure of Structure of E Coli Hydrogenase Hyd-1 Mutant E28Q, PDB code: 5lmm was solved by S.B.Carr, S.E.V.Phillips, R.M.Evans, E.J.Brooke, F.A.Armstrong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 91.74 / 1.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 93.981, 97.799, 183.474, 90.00, 90.00, 90.00
R / Rfree (%) 11.8 / 14.6

Other elements in 5lmm:

The structure of Structure of E Coli Hydrogenase Hyd-1 Mutant E28Q 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 - 26;

Binding sites:

The binding sites of Iron atom in the Structure of E Coli Hydrogenase Hyd-1 Mutant E28Q (pdb code 5lmm). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 26 binding sites of Iron where determined in the Structure of E Coli Hydrogenase Hyd-1 Mutant E28Q, PDB code: 5lmm:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 26 in 5lmm

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Iron binding site 1 out of 26 in the Structure of E Coli Hydrogenase Hyd-1 Mutant E28Q


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of E Coli Hydrogenase Hyd-1 Mutant E28Q within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe401

b:8.7
occ:1.00
FE1 S:SF4401 0.0 8.7 1.0
S2 S:SF4401 2.3 9.3 1.0
SG S:CYS215 2.3 9.1 1.0
S3 S:SF4401 2.3 8.7 1.0
S4 S:SF4401 2.3 9.2 1.0
FE3 S:SF4401 2.7 9.1 1.0
FE4 S:SF4401 2.7 8.9 1.0
FE2 S:SF4401 2.8 8.5 1.0
CB S:CYS215 3.4 9.1 1.0
N S:LEU216 3.8 7.9 1.0
S1 S:SF4401 3.9 8.9 1.0
CA S:CYS215 3.9 8.2 1.0
N S:TYR217 4.2 8.4 1.0
CB S:PHE196 4.3 9.7 1.0
C S:CYS215 4.3 8.1 1.0
CD1 S:PHE196 4.4 10.8 1.0
ND1 S:HIS187 4.5 9.7 1.0
CB S:TYR217 4.6 9.8 1.0
CB S:ARG192 4.7 8.5 1.0
O S:ARG192 4.8 9.1 1.0
CA S:LEU216 4.8 8.5 1.0
CE1 S:HIS187 4.8 11.6 1.0
CG S:PHE196 4.8 10.5 1.0
C S:LEU216 4.8 8.9 1.0
CA S:TYR217 4.8 8.5 1.0
SG S:CYS190 4.9 8.9 1.0
SG S:CYS221 4.9 8.3 1.0

Iron binding site 2 out of 26 in 5lmm

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Iron binding site 2 out of 26 in the Structure of E Coli Hydrogenase Hyd-1 Mutant E28Q


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of E Coli Hydrogenase Hyd-1 Mutant E28Q within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe401

b:8.5
occ:1.00
FE2 S:SF4401 0.0 8.5 1.0
S4 S:SF4401 2.3 9.2 1.0
S1 S:SF4401 2.3 8.9 1.0
SG S:CYS221 2.3 8.3 1.0
S3 S:SF4401 2.3 8.7 1.0
FE4 S:SF4401 2.7 8.9 1.0
FE3 S:SF4401 2.7 9.1 1.0
FE1 S:SF4401 2.8 8.7 1.0
CB S:CYS221 3.2 9.1 1.0
S2 S:SF4401 3.9 9.3 1.0
CD1 S:ILE243 4.0 9.2 1.0
CG1 S:ILE243 4.5 8.8 1.0
CD S:PRO224 4.5 9.5 1.0
N S:GLY223 4.5 8.7 1.0
CA S:GLY223 4.6 9.0 1.0
CA S:CYS221 4.6 8.6 1.0
ND1 S:HIS187 4.7 9.7 1.0
SG S:CYS215 4.7 9.1 1.0
N S:TYR217 4.8 8.4 1.0
SG S:CYS190 4.8 8.9 1.0
N S:LEU216 4.9 7.9 1.0
C S:CYS221 4.9 8.8 1.0
CB S:LEU216 4.9 8.4 1.0
C S:LEU216 5.0 8.9 1.0
O S:CYS221 5.0 8.8 1.0

Iron binding site 3 out of 26 in 5lmm

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Iron binding site 3 out of 26 in the Structure of E Coli Hydrogenase Hyd-1 Mutant E28Q


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of E Coli Hydrogenase Hyd-1 Mutant E28Q within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe401

b:9.1
occ:1.00
FE3 S:SF4401 0.0 9.1 1.0
ND1 S:HIS187 2.1 9.7 1.0
S1 S:SF4401 2.3 8.9 1.0
S4 S:SF4401 2.3 9.2 1.0
S2 S:SF4401 2.3 9.3 1.0
FE4 S:SF4401 2.7 8.9 1.0
FE1 S:SF4401 2.7 8.7 1.0
FE2 S:SF4401 2.7 8.5 1.0
CE1 S:HIS187 2.9 11.6 1.0
CG S:HIS187 3.2 11.1 1.0
CB S:HIS187 3.7 10.2 1.0
S3 S:SF4401 3.9 8.7 1.0
CA S:HIS187 4.1 8.5 1.0
NE2 S:HIS187 4.1 12.5 1.0
CD2 S:HIS187 4.2 13.6 1.0
CG S:PRO224 4.3 10.2 1.0
CD S:PRO224 4.3 9.5 1.0
CD S:ARG193 4.3 15.6 0.5
CB S:CYS190 4.6 8.7 1.0
SG S:CYS215 4.7 9.1 1.0
SG S:CYS190 4.7 8.9 1.0
O S:HIS187 4.8 13.8 1.0
CD1 S:PHE196 4.8 10.8 1.0
SG S:CYS221 4.8 8.3 1.0
N S:PRO224 4.8 9.8 1.0
CD S:ARG193 4.9 17.2 0.5
CG S:ARG193 4.9 13.8 0.5
C S:HIS187 5.0 10.1 1.0

Iron binding site 4 out of 26 in 5lmm

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Iron binding site 4 out of 26 in the Structure of E Coli Hydrogenase Hyd-1 Mutant E28Q


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of E Coli Hydrogenase Hyd-1 Mutant E28Q within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe401

b:8.9
occ:1.00
FE4 S:SF4401 0.0 8.9 1.0
SG S:CYS190 2.3 8.9 1.0
S2 S:SF4401 2.3 9.3 1.0
S3 S:SF4401 2.3 8.7 1.0
S1 S:SF4401 2.3 8.9 1.0
FE3 S:SF4401 2.7 9.1 1.0
FE2 S:SF4401 2.7 8.5 1.0
FE1 S:SF4401 2.7 8.7 1.0
CB S:CYS190 3.1 8.7 1.0
S4 S:SF4401 3.9 9.2 1.0
CB S:ARG192 4.2 8.5 1.0
CD1 S:ILE243 4.3 9.2 1.0
CG2 S:ILE243 4.3 9.0 1.0
ND1 S:HIS187 4.5 9.7 1.0
CA S:CYS190 4.6 7.8 1.0
C S:ARG192 4.7 8.4 1.0
N S:ARG192 4.7 8.0 1.0
CA S:ARG192 4.7 8.8 1.0
N S:ARG193 4.8 8.8 0.5
N S:ARG193 4.8 8.9 0.5
SG S:CYS221 4.8 8.3 1.0
CG1 S:ILE243 4.9 8.8 1.0
SG S:CYS215 4.9 9.1 1.0
C S:CYS190 5.0 7.5 1.0

Iron binding site 5 out of 26 in 5lmm

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Iron binding site 5 out of 26 in the Structure of E Coli Hydrogenase Hyd-1 Mutant E28Q


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structure of E Coli Hydrogenase Hyd-1 Mutant E28Q within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe402

b:10.0
occ:1.00
FE1 S:F3S402 0.0 10.0 1.0
S1 S:F3S402 2.2 9.6 1.0
S2 S:F3S402 2.3 10.3 1.0
SG S:CYS252 2.3 10.5 1.0
S3 S:F3S402 2.3 9.7 1.0
FE3 S:F3S402 2.7 9.1 1.0
FE4 S:F3S402 2.7 9.3 1.0
CB S:CYS252 3.4 9.4 1.0
O L:HOH718 3.8 12.7 1.0
N S:CYS252 3.8 8.4 1.0
S4 S:F3S402 3.9 10.3 1.0
O S:HOH603 4.0 9.7 1.0
CA S:CYS252 4.1 9.2 1.0
NZ L:LYS226 4.2 14.6 0.5
N S:ALA253 4.5 9.1 1.0
O L:HOH1001 4.5 11.9 1.0
C S:CYS252 4.6 8.9 1.0
ND2 S:ASN228 4.7 8.9 1.0
SG S:CYS230 4.7 8.9 1.0
SG S:CYS249 4.7 9.2 1.0
C S:GLY251 5.0 8.3 1.0

Iron binding site 6 out of 26 in 5lmm

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Iron binding site 6 out of 26 in the Structure of E Coli Hydrogenase Hyd-1 Mutant E28Q


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Structure of E Coli Hydrogenase Hyd-1 Mutant E28Q within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe402

b:9.1
occ:1.00
FE3 S:F3S402 0.0 9.1 1.0
S4 S:F3S402 2.2 10.3 1.0
S1 S:F3S402 2.2 9.6 1.0
S3 S:F3S402 2.3 9.7 1.0
SG S:CYS230 2.3 8.9 1.0
FE1 S:F3S402 2.7 10.0 1.0
FE4 S:F3S402 2.7 9.3 1.0
CB S:CYS230 3.3 8.5 1.0
S2 S:F3S402 3.9 10.3 1.0
ND2 S:ASN228 4.0 8.9 1.0
O S:HOH603 4.3 9.7 1.0
CD1 S:ILE186 4.3 13.3 1.0
NE1 S:TRP235 4.3 8.0 1.0
CD S:PRO242 4.5 7.8 1.0
CG S:PRO242 4.6 8.6 1.0
CG S:ASN228 4.7 8.2 1.0
CA S:CYS230 4.7 7.8 1.0
SG S:CYS252 4.8 10.5 1.0
CB S:ASN228 4.8 8.2 1.0
SG S:CYS249 4.8 9.2 1.0
CG1 S:ILE186 4.8 11.5 1.0

Iron binding site 7 out of 26 in 5lmm

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Iron binding site 7 out of 26 in the Structure of E Coli Hydrogenase Hyd-1 Mutant E28Q


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Structure of E Coli Hydrogenase Hyd-1 Mutant E28Q within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe402

b:9.3
occ:1.00
FE4 S:F3S402 0.0 9.3 1.0
S4 S:F3S402 2.2 10.3 1.0
S2 S:F3S402 2.3 10.3 1.0
SG S:CYS249 2.3 9.2 1.0
S3 S:F3S402 2.3 9.7 1.0
FE1 S:F3S402 2.7 10.0 1.0
FE3 S:F3S402 2.7 9.1 1.0
CB S:CYS249 3.3 7.9 1.0
CA S:CYS249 3.7 7.6 1.0
S1 S:F3S402 3.9 9.6 1.0
N S:LEU250 4.0 8.2 1.0
N S:GLY251 4.2 9.0 1.0
C S:CYS249 4.3 7.7 1.0
N S:CYS252 4.4 8.4 1.0
CG2 S:THR226 4.6 9.6 1.0
CA S:GLY251 4.8 9.5 1.0
SG S:CYS252 4.8 10.5 1.0
CG1 S:ILE186 4.8 11.5 1.0
SG S:CYS230 4.8 8.9 1.0
CG S:PRO242 4.9 8.6 1.0
N S:CYS249 5.0 8.0 1.0

Iron binding site 8 out of 26 in 5lmm

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Iron binding site 8 out of 26 in the Structure of E Coli Hydrogenase Hyd-1 Mutant E28Q


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Structure of E Coli Hydrogenase Hyd-1 Mutant E28Q within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe403

b:10.7
occ:0.90
FE1 S:SF3403 0.0 10.7 0.9
S1 S:SF3403 2.2 9.8 0.9
S2 S:SF3403 2.3 10.9 0.9
SG S:CYS115 2.3 10.8 1.0
S3 S:SF3403 2.3 10.2 0.9
FE4 S:SF3403 2.6 11.6 0.9
FE3 S:SF3403 2.7 8.6 0.9
CB S:CYS115 3.3 10.6 1.0
O S:HOH526 3.4 16.6 0.5
FE7 S:SF3403 3.6 16.1 0.5
O L:HOH726 3.8 13.4 0.9
O S:HOH518 3.9 14.0 1.0
FE7 S:SF3403 3.9 9.7 0.5
N S:CYS115 4.0 8.5 1.0
SG S:CYS19 4.1 10.7 1.0
CA S:CYS115 4.2 8.8 1.0
O S:HOH590 4.2 9.7 1.0
SG S:CYS120 4.4 10.2 1.0
CB S:CYS120 4.4 8.6 1.0
N S:CYS17 4.6 10.1 1.0
SG S:CYS149 4.7 9.2 1.0
SG S:CYS17 4.7 10.7 1.0
SG S:CYS20 4.7 10.9 1.0
CA S:GLU16 4.9 10.6 1.0
CB S:GLU16 4.9 12.6 1.0

Iron binding site 9 out of 26 in 5lmm

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Iron binding site 9 out of 26 in the Structure of E Coli Hydrogenase Hyd-1 Mutant E28Q


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Structure of E Coli Hydrogenase Hyd-1 Mutant E28Q within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe403

b:8.6
occ:0.90
FE3 S:SF3403 0.0 8.6 0.9
S1 S:SF3403 2.3 9.8 0.9
S3 S:SF3403 2.3 10.2 0.9
SG S:CYS149 2.3 9.2 1.0
SG S:CYS120 2.3 10.2 1.0
FE1 S:SF3403 2.7 10.7 0.9
CB S:CYS149 3.3 8.3 1.0
CB S:CYS120 3.5 8.6 1.0
FE4 S:SF3403 3.6 11.6 0.9
O L:HOH726 3.7 13.4 0.9
CA S:CYS149 4.0 7.4 1.0
SG S:CYS115 4.0 10.8 1.0
SG S:CYS19 4.4 10.7 1.0
CG L:ARG74 4.4 8.4 1.0
N S:CYS115 4.5 8.5 1.0
CB S:THR114 4.6 9.1 1.0
S2 S:SF3403 4.7 10.9 0.9
CA S:CYS120 4.9 8.6 1.0
C S:CYS149 4.9 7.7 1.0
N S:VAL121 4.9 7.9 1.0
O S:GLY148 4.9 8.5 1.0

Iron binding site 10 out of 26 in 5lmm

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Iron binding site 10 out of 26 in the Structure of E Coli Hydrogenase Hyd-1 Mutant E28Q


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Structure of E Coli Hydrogenase Hyd-1 Mutant E28Q within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Fe403

b:11.6
occ:0.90
FE4 S:SF3403 0.0 11.6 0.9
O L:HOH726 1.6 13.4 0.9
SG S:CYS17 2.3 10.7 1.0
S3 S:SF3403 2.3 10.2 0.9
S2 S:SF3403 2.3 10.9 0.9
SG S:CYS19 2.4 10.7 1.0
FE1 S:SF3403 2.6 10.7 0.9
FE7 S:SF3403 3.0 16.1 0.5
FE7 S:SF3403 3.2 9.7 0.5
CB S:CYS17 3.4 9.9 1.0
CB S:CYS19 3.5 9.0 1.0
FE3 S:SF3403 3.6 8.6 0.9
S1 S:SF3403 3.7 9.8 0.9
N S:CYS19 3.8 8.9 1.0
N S:CYS17 3.8 10.1 1.0
O S:HOH526 3.9 16.6 0.5
CA S:CYS17 4.0 9.6 1.0
NE2 L:HIS229 4.1 12.6 1.0
CA S:CYS19 4.2 8.8 1.0
N S:THR18 4.3 9.4 1.0
C S:CYS17 4.3 9.5 1.0
SG S:CYS149 4.4 9.2 1.0
SG S:CYS115 4.6 10.8 1.0
O S:HOH590 4.6 9.7 1.0
OE2 S:GLU76 4.7 14.0 0.5
N S:CYS20 4.8 9.2 1.0
CD2 L:HIS229 4.8 9.6 1.0
C S:THR18 4.9 8.8 1.0
C S:GLU16 5.0 10.3 1.0

Reference:

S.B.Carr, S.E.V.Phillips, R.M.Evans, E.J.Brooke, S.T.A.Islam, G.M.Roberts, S.A.M.Wehlin, F.A.Armstrong. Kinetic Consequences of Re-Engineering the Outer Shell "Canopy" Above the Active Site of A [Nife]-Hydrogenase. To Be Published.
Page generated: Tue Aug 6 04:42:44 2024

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