Atomistry » Iron » PDB 4bmq-4ccp » 4c3o
Atomistry »
  Iron »
    PDB 4bmq-4ccp »
      4c3o »

Iron in PDB 4c3o: Structure and Function of An Oxygen Tolerant Nife Hydrogenase From Salmonella

Enzymatic activity of Structure and Function of An Oxygen Tolerant Nife Hydrogenase From Salmonella

All present enzymatic activity of Structure and Function of An Oxygen Tolerant Nife Hydrogenase From Salmonella:
1.12.7.2;

Protein crystallography data

The structure of Structure and Function of An Oxygen Tolerant Nife Hydrogenase From Salmonella, PDB code: 4c3o was solved by L.Bowman, L.Flanagan, P.K.Fyfe, A.Parkin, W.N.Hunter, F.Sargent, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.52 / 3.20
Space group I 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 115.460, 122.210, 227.820, 90.00, 95.56, 90.00
R / Rfree (%) 15.811 / 20.467

Other elements in 4c3o:

The structure of Structure and Function of An Oxygen Tolerant Nife Hydrogenase From Salmonella also contains other interesting chemical elements:

Nickel (Ni) 3 atoms
Magnesium (Mg) 3 atoms
Chlorine (Cl) 6 atoms

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 36;

Binding sites:

The binding sites of Iron atom in the Structure and Function of An Oxygen Tolerant Nife Hydrogenase From Salmonella (pdb code 4c3o). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 36 binding sites of Iron where determined in the Structure and Function of An Oxygen Tolerant Nife Hydrogenase From Salmonella, PDB code: 4c3o:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 36 in 4c3o

Go back to Iron Binding Sites List in 4c3o
Iron binding site 1 out of 36 in the Structure and Function of An Oxygen Tolerant Nife Hydrogenase From Salmonella


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure and Function of An Oxygen Tolerant Nife Hydrogenase From Salmonella within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe1003

b:94.8
occ:1.00
FE2 F:F4S1003 0.0 94.8 1.0
SG F:CYS115 2.2 89.5 1.0
S2 F:F4S1003 2.3 0.5 1.0
S1 F:F4S1003 2.3 0.7 1.0
S3 F:F4S1003 2.3 87.7 1.0
FE3 F:F4S1003 2.7 79.4 1.0
FE4 F:F4S1003 2.7 0.4 1.0
FE1 F:F4S1003 3.1 95.6 1.0
CB F:CYS115 3.4 86.7 1.0
O E:HOH2002 4.0 47.7 1.0
O F:HOH2003 4.2 82.7 1.0
SG F:CYS120 4.2 76.2 1.0
N F:CYS17 4.3 75.0 1.0
SG F:CYS19 4.3 97.1 1.0
N F:CYS115 4.3 78.2 1.0
SG F:CYS17 4.4 79.2 1.0
CA F:CYS115 4.4 82.9 1.0
SG F:CYS149 4.5 73.5 1.0
CB F:CYS120 4.5 75.7 1.0
CA F:GLU16 4.5 81.7 1.0
SG F:CYS20 4.8 80.8 1.0
CB F:GLU16 4.8 82.0 1.0
C F:GLU16 4.9 81.5 1.0
CB F:CYS17 5.0 78.9 1.0

Iron binding site 2 out of 36 in 4c3o

Go back to Iron Binding Sites List in 4c3o
Iron binding site 2 out of 36 in the Structure and Function of An Oxygen Tolerant Nife Hydrogenase From Salmonella


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure and Function of An Oxygen Tolerant Nife Hydrogenase From Salmonella within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe1003

b:79.4
occ:1.00
FE3 F:F4S1003 0.0 79.4 1.0
S3 F:F4S1003 2.3 87.7 1.0
S2 F:F4S1003 2.3 0.5 1.0
SG F:CYS149 2.3 73.5 1.0
SG F:CYS120 2.3 76.2 1.0
FE2 F:F4S1003 2.7 94.8 1.0
CB F:CYS149 3.3 75.4 1.0
CB F:CYS120 3.4 75.7 1.0
FE4 F:F4S1003 3.6 0.4 1.0
CA F:CYS149 3.7 70.5 1.0
SG F:CYS115 3.8 89.5 1.0
N F:CYS115 4.0 78.2 1.0
CB F:SER114 4.1 72.3 1.0
FE1 F:F4S1003 4.1 95.6 1.0
N F:SER114 4.3 74.8 1.0
SG F:CYS19 4.5 97.1 1.0
S1 F:F4S1003 4.5 0.7 1.0
CA F:SER114 4.6 73.9 1.0
O F:GLY148 4.6 66.0 1.0
CB F:CYS115 4.6 86.7 1.0
C F:SER114 4.6 76.5 1.0
CA F:CYS115 4.7 82.9 1.0
C F:CYS149 4.7 64.8 1.0
N F:CYS149 4.7 68.5 1.0
CA F:CYS120 4.9 74.5 1.0

Iron binding site 3 out of 36 in 4c3o

Go back to Iron Binding Sites List in 4c3o
Iron binding site 3 out of 36 in the Structure and Function of An Oxygen Tolerant Nife Hydrogenase From Salmonella


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure and Function of An Oxygen Tolerant Nife Hydrogenase From Salmonella within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe1003

b:0.4
occ:1.00
FE4 F:F4S1003 0.0 0.4 1.0
SG F:CYS17 2.2 79.2 1.0
S3 F:F4S1003 2.3 87.7 1.0
SG F:CYS19 2.3 97.1 1.0
S1 F:F4S1003 2.3 0.7 1.0
FE2 F:F4S1003 2.7 94.8 1.0
FE1 F:F4S1003 2.8 95.6 1.0
CB F:CYS19 3.1 89.8 1.0
NE2 E:HIS229 3.3 77.1 1.0
S2 F:F4S1003 3.5 0.5 1.0
FE3 F:F4S1003 3.6 79.4 1.0
CB F:CYS17 3.7 78.9 1.0
SG F:CYS149 3.9 73.5 1.0
N F:CYS19 4.0 83.2 1.0
CD2 E:HIS229 4.1 76.9 1.0
CA F:CYS19 4.1 83.3 1.0
N F:CYS17 4.2 75.0 1.0
CA F:CYS17 4.3 76.8 1.0
CE1 E:HIS229 4.4 73.3 1.0
C F:CYS17 4.5 75.2 1.0
N F:THR18 4.8 80.0 1.0
O E:HOH2002 4.9 47.7 1.0
C F:CYS19 4.9 75.2 1.0
SG F:CYS115 4.9 89.5 1.0
O F:CYS17 4.9 75.0 1.0
N F:CYS20 4.9 72.2 1.0

Iron binding site 4 out of 36 in 4c3o

Go back to Iron Binding Sites List in 4c3o
Iron binding site 4 out of 36 in the Structure and Function of An Oxygen Tolerant Nife Hydrogenase From Salmonella


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure and Function of An Oxygen Tolerant Nife Hydrogenase From Salmonella within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe1003

b:95.6
occ:1.00
FE1 F:F4S1003 0.0 95.6 1.0
SG F:CYS20 2.3 80.8 1.0
S1 F:F4S1003 2.3 0.7 1.0
S2 F:F4S1003 2.3 0.5 1.0
SG F:CYS19 2.4 97.1 1.0
FE4 F:F4S1003 2.8 0.4 1.0
N F:CYS20 2.9 72.2 1.0
FE2 F:F4S1003 3.1 94.8 1.0
N F:CYS19 3.4 83.2 1.0
CB F:CYS19 3.5 89.8 1.0
C F:CYS19 3.6 75.2 1.0
OE2 F:GLU76 3.6 91.3 1.0
CA F:CYS19 3.6 83.3 1.0
CB F:CYS20 3.7 78.7 1.0
CA F:CYS20 3.9 78.5 1.0
FE3 F:F4S1003 4.1 79.4 1.0
O F:HOH2003 4.2 82.7 1.0
S3 F:F4S1003 4.3 87.7 1.0
SG F:CYS17 4.6 79.2 1.0
C F:THR18 4.6 82.2 1.0
O F:CYS19 4.7 71.0 1.0
CD F:GLU76 4.7 86.5 1.0
CB F:PRO150 4.8 55.6 1.0
CA F:PRO150 5.0 58.4 1.0
N F:THR18 5.0 80.0 1.0

Iron binding site 5 out of 36 in 4c3o

Go back to Iron Binding Sites List in 4c3o
Iron binding site 5 out of 36 in the Structure and Function of An Oxygen Tolerant Nife Hydrogenase From Salmonella


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structure and Function of An Oxygen Tolerant Nife Hydrogenase From Salmonella within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1004

b:71.6
occ:1.00
FE A:NFU1004 0.0 71.6 1.0
C3 A:NFU1004 1.7 69.8 1.0
C1 A:NFU1004 1.9 78.7 1.0
C2 A:NFU1004 1.9 70.4 1.0
SG A:CYS582 2.1 75.1 1.0
SG A:CYS79 2.4 74.0 1.0
CB A:CYS79 2.5 68.7 1.0
NI A:NFU1004 2.9 73.0 1.0
O3 A:NFU1004 2.9 71.4 1.0
N1 A:NFU1004 3.1 80.9 1.0
N2 A:NFU1004 3.1 73.7 1.0
CB A:CYS582 3.4 68.0 1.0
CD A:ARG512 3.9 64.6 1.0
CA A:CYS79 4.1 71.1 1.0
NH1 A:ARG512 4.2 62.2 1.0
CG1 A:VAL533 4.5 71.9 1.0
CG2 A:THR82 4.6 71.4 1.0
CB A:CYS579 4.7 72.7 1.0
CB A:ARG512 4.7 66.1 1.0
NE2 A:HIS83 4.7 70.8 1.0
SG A:CYS579 4.8 70.3 1.0
CB A:ALA510 4.8 69.6 1.0
O A:CYS79 4.8 79.1 1.0
CA A:CYS582 4.8 68.3 1.0
NE A:ARG512 4.8 61.4 1.0
CD A:PRO534 4.8 65.9 1.0
CG A:ARG512 4.9 66.4 1.0
SG A:CYS76 4.9 62.4 1.0
N A:CYS79 5.0 69.2 1.0
CZ A:ARG512 5.0 59.7 1.0

Iron binding site 6 out of 36 in 4c3o

Go back to Iron Binding Sites List in 4c3o
Iron binding site 6 out of 36 in the Structure and Function of An Oxygen Tolerant Nife Hydrogenase From Salmonella


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Structure and Function of An Oxygen Tolerant Nife Hydrogenase From Salmonella within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1001

b:78.9
occ:1.00
FE1 B:SF41001 0.0 78.9 1.0
ND1 B:HIS187 2.0 79.3 1.0
S4 B:SF41001 2.3 74.7 1.0
S3 B:SF41001 2.3 66.3 1.0
S2 B:SF41001 2.3 79.6 1.0
FE4 B:SF41001 2.7 73.0 1.0
FE2 B:SF41001 2.7 69.9 1.0
CE1 B:HIS187 2.7 81.5 1.0
FE3 B:SF41001 2.7 66.4 1.0
CG B:HIS187 3.1 73.8 1.0
CB B:HIS187 3.7 73.5 1.0
S1 B:SF41001 3.9 76.9 1.0
NE2 B:HIS187 3.9 77.7 1.0
CD2 B:HIS187 4.1 72.7 1.0
CA B:HIS187 4.2 71.4 1.0
SG B:CYS215 4.4 73.0 1.0
CD B:PRO224 4.5 68.6 1.0
SG B:CYS190 4.6 68.4 1.0
CB B:CYS190 4.6 70.7 1.0
CD2 B:PHE196 4.6 79.7 1.0
O B:HIS187 4.7 64.0 1.0
CD B:ARG193 4.7 77.6 1.0
SG B:CYS221 4.8 67.3 1.0
CG B:PHE196 4.9 78.2 1.0
C B:HIS187 4.9 68.4 1.0
CB B:PHE196 5.0 79.3 1.0

Iron binding site 7 out of 36 in 4c3o

Go back to Iron Binding Sites List in 4c3o
Iron binding site 7 out of 36 in the Structure and Function of An Oxygen Tolerant Nife Hydrogenase From Salmonella


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Structure and Function of An Oxygen Tolerant Nife Hydrogenase From Salmonella within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1001

b:69.9
occ:1.00
FE2 B:SF41001 0.0 69.9 1.0
S1 B:SF41001 2.3 76.9 1.0
S3 B:SF41001 2.3 66.3 1.0
S4 B:SF41001 2.3 74.7 1.0
SG B:CYS190 2.3 68.4 1.0
FE1 B:SF41001 2.7 78.9 1.0
FE3 B:SF41001 2.7 66.4 1.0
FE4 B:SF41001 2.7 73.0 1.0
CB B:CYS190 3.3 70.7 1.0
S2 B:SF41001 3.9 79.6 1.0
CB B:ARG192 4.1 69.7 1.0
CD1 B:ILE243 4.2 74.0 1.0
CG2 B:ILE243 4.4 61.2 1.0
ND1 B:HIS187 4.5 79.3 1.0
C B:ARG192 4.6 72.6 1.0
N B:ARG193 4.6 74.5 1.0
CA B:ARG192 4.7 71.3 1.0
N B:ARG192 4.7 69.9 1.0
CA B:CYS190 4.7 72.0 1.0
SG B:CYS215 4.8 73.0 1.0
SG B:CYS221 4.9 67.3 1.0
O B:ARG192 4.9 67.9 1.0
CA B:ARG193 4.9 73.8 1.0

Iron binding site 8 out of 36 in 4c3o

Go back to Iron Binding Sites List in 4c3o
Iron binding site 8 out of 36 in the Structure and Function of An Oxygen Tolerant Nife Hydrogenase From Salmonella


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Structure and Function of An Oxygen Tolerant Nife Hydrogenase From Salmonella within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1001

b:66.4
occ:1.00
FE3 B:SF41001 0.0 66.4 1.0
SG B:CYS221 2.3 67.3 1.0
S1 B:SF41001 2.3 76.9 1.0
S2 B:SF41001 2.3 79.6 1.0
S4 B:SF41001 2.3 74.7 1.0
FE4 B:SF41001 2.7 73.0 1.0
FE2 B:SF41001 2.7 69.9 1.0
FE1 B:SF41001 2.7 78.9 1.0
CB B:CYS221 3.5 71.1 1.0
CD1 B:ILE243 3.6 74.0 1.0
S3 B:SF41001 3.9 66.3 1.0
CA B:GLY223 4.3 63.0 1.0
N B:GLY223 4.3 62.3 1.0
ND1 B:HIS187 4.4 79.3 1.0
CG1 B:ILE243 4.5 71.7 1.0
CD B:PRO224 4.5 68.6 1.0
SG B:CYS190 4.6 68.4 1.0
CA B:CYS221 4.8 73.8 1.0
SG B:CYS215 4.9 73.0 1.0
C B:CYS221 5.0 68.8 1.0

Iron binding site 9 out of 36 in 4c3o

Go back to Iron Binding Sites List in 4c3o
Iron binding site 9 out of 36 in the Structure and Function of An Oxygen Tolerant Nife Hydrogenase From Salmonella


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Structure and Function of An Oxygen Tolerant Nife Hydrogenase From Salmonella within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1001

b:73.0
occ:1.00
FE4 B:SF41001 0.0 73.0 1.0
SG B:CYS215 2.3 73.0 1.0
S1 B:SF41001 2.3 76.9 1.0
S3 B:SF41001 2.3 66.3 1.0
S2 B:SF41001 2.3 79.6 1.0
FE1 B:SF41001 2.7 78.9 1.0
FE3 B:SF41001 2.7 66.4 1.0
FE2 B:SF41001 2.7 69.9 1.0
CB B:CYS215 3.4 72.3 1.0
N B:LEU216 3.6 70.9 1.0
CA B:CYS215 3.9 70.0 1.0
S4 B:SF41001 3.9 74.7 1.0
N B:TYR217 3.9 78.9 1.0
C B:CYS215 4.1 72.5 1.0
CB B:TYR217 4.3 81.0 1.0
CD2 B:PHE196 4.5 79.7 1.0
SG B:CYS221 4.5 67.3 1.0
CA B:TYR217 4.5 79.2 1.0
ND1 B:HIS187 4.5 79.3 1.0
CA B:LEU216 4.5 72.7 1.0
C B:LEU216 4.6 77.3 1.0
CB B:PHE196 4.6 79.3 1.0
CE1 B:HIS187 4.8 81.5 1.0
CB B:CYS221 4.8 71.1 1.0
CB B:LEU216 4.9 67.5 1.0
CG B:PHE196 4.9 78.2 1.0

Iron binding site 10 out of 36 in 4c3o

Go back to Iron Binding Sites List in 4c3o
Iron binding site 10 out of 36 in the Structure and Function of An Oxygen Tolerant Nife Hydrogenase From Salmonella


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Structure and Function of An Oxygen Tolerant Nife Hydrogenase From Salmonella within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1002

b:59.7
occ:1.00
FE1 B:F3S1002 0.0 59.7 1.0
S3 B:F3S1002 2.2 61.4 1.0
S2 B:F3S1002 2.2 52.0 1.0
S1 B:F3S1002 2.2 76.1 1.0
SG B:CYS249 2.3 72.4 1.0
FE4 B:F3S1002 2.6 52.1 1.0
FE3 B:F3S1002 2.7 66.5 1.0
CB B:CYS249 3.6 72.5 1.0
N B:LEU250 3.8 75.6 1.0
CA B:CYS249 3.9 72.4 1.0
CD1 B:ILE186 3.9 65.5 1.0
N B:GLY251 4.0 68.7 1.0
S4 B:F3S1002 4.0 63.4 1.0
N B:CYS252 4.2 67.0 1.0
C B:CYS249 4.3 72.7 1.0
SG B:CYS252 4.4 64.8 1.0
CA B:GLY251 4.5 67.5 1.0
CG2 B:THR226 4.5 71.5 1.0
SG B:CYS230 4.8 59.3 1.0
C B:GLY251 4.8 63.8 1.0
CA B:LEU250 4.8 74.8 1.0
CG B:PRO242 4.9 56.2 1.0
C B:LEU250 4.9 73.3 1.0

Reference:

L.Bowman, L.Flanagan, P.K.Fyfe, A.Parkin, W.N.Hunter, F.Sargent. How the Structure of the Large Subunit Controls Function in An Oxygen-Tolerant [Nife]-Hydrogenase. Biochem.J. V. 458 449 2014.
ISSN: ISSN 0264-6021
PubMed: 24428762
DOI: 10.1042/BJ20131520
Page generated: Sun Dec 13 15:29:35 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy