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Iron in PDB 5vq3: Nitrogenase CP1 at pH 6.5

Enzymatic activity of Nitrogenase CP1 at pH 6.5

All present enzymatic activity of Nitrogenase CP1 at pH 6.5:
1.18.6.1;

Protein crystallography data

The structure of Nitrogenase CP1 at pH 6.5, PDB code: 5vq3 was solved by C.N.Morrison, T.Spatzal, D.C.Rees, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.72
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 69.477, 147.963, 116.694, 90.00, 103.51, 90.00
R / Rfree (%) 15.9 / 18.5

Other elements in 5vq3:

The structure of Nitrogenase CP1 at pH 6.5 also contains other interesting chemical elements:

Molybdenum (Mo) 2 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 Nitrogenase CP1 at pH 6.5 (pdb code 5vq3). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 32 binding sites of Iron where determined in the Nitrogenase CP1 at pH 6.5, PDB code: 5vq3:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 32 in 5vq3

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Iron binding site 1 out of 32 in the Nitrogenase CP1 at pH 6.5


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Nitrogenase CP1 at pH 6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:21.1
occ:1.00
 FE1 A:ICS602 0.0 21.1 1.0
S2A A:ICS602 2.3 20.7 1.0
S1A A:ICS602 2.3 21.5 1.0
SG A:CYS262 2.3 20.5 1.0
S4A A:ICS602 2.3 21.1 1.0
FE4 A:ICS602 2.6 20.2 1.0
FE2 A:ICS602 2.7 19.3 1.0
FE3 A:ICS602 2.7 20.2 1.0
CB A:CYS262 3.3 20.0 1.0
CX A:ICS602 3.5 19.6 1.0
OG A:SER265 3.9 20.4 1.0
CB A:SER346 4.1 25.1 0.5
CB A:SER346 4.1 25.8 0.5
CB A:SER265 4.1 22.8 1.0
CA A:CYS262 4.6 22.2 1.0
CE2 A:TYR216 4.7 21.5 1.0
O A:HOH764 4.7 27.4 1.0
N A:SER265 4.8 22.4 1.0
S3A A:ICS602 4.8 19.7 1.0
OG A:SER346 4.8 28.4 0.5
OG A:SER346 4.8 29.6 0.5
S2B A:ICS602 4.9 19.7 1.0
O A:HOH756 4.9 37.4 1.0
S5A A:ICS602 4.9 21.7 1.0
FE5 A:ICS602 5.0 18.5 1.0

Iron binding site 2 out of 32 in 5vq3

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Iron binding site 2 out of 32 in the Nitrogenase CP1 at pH 6.5


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Nitrogenase CP1 at pH 6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:19.3
occ:1.00
 FE2 A:ICS602 0.0 19.3 1.0
CX A:ICS602 2.0 19.6 1.0
S2A A:ICS602 2.2 20.7 1.0
S2B A:ICS602 2.2 19.7 1.0
S1A A:ICS602 2.3 21.5 1.0
FE6 A:ICS602 2.6 18.9 1.0
FE4 A:ICS602 2.7 20.2 1.0
FE3 A:ICS602 2.7 20.2 1.0
FE1 A:ICS602 2.7 21.1 1.0
FE5 A:ICS602 3.7 18.5 1.0
FE7 A:ICS602 3.7 19.4 1.0
S4A A:ICS602 3.9 21.1 1.0
NE2 A:HIS186 3.9 21.1 1.0
CZ A:PHE369 4.0 25.4 1.0
CE1 A:HIS186 4.0 22.0 1.0
S1B A:ICS602 4.2 19.6 1.0
S3B A:ICS602 4.2 19.5 1.0
CG1 A:VAL61 4.3 22.8 1.0
CE1 A:PHE369 4.5 25.9 1.0
S3A A:ICS602 4.5 19.7 1.0
S5A A:ICS602 4.5 21.7 1.0
SG A:CYS262 4.8 20.5 1.0
CB A:SER265 4.9 22.8 1.0

Iron binding site 3 out of 32 in 5vq3

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Iron binding site 3 out of 32 in the Nitrogenase CP1 at pH 6.5


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Nitrogenase CP1 at pH 6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:20.2
occ:1.00
 FE3 A:ICS602 0.0 20.2 1.0
CX A:ICS602 2.0 19.6 1.0
S5A A:ICS602 2.2 21.7 1.0
S4A A:ICS602 2.3 21.1 1.0
S2A A:ICS602 2.3 20.7 1.0
FE7 A:ICS602 2.6 19.4 1.0
FE2 A:ICS602 2.7 19.3 1.0
FE4 A:ICS602 2.7 20.2 1.0
FE1 A:ICS602 2.7 21.1 1.0
FE5 A:ICS602 3.7 18.5 1.0
FE6 A:ICS602 3.7 18.9 1.0
S1A A:ICS602 3.9 21.5 1.0
S3B A:ICS602 4.2 19.5 1.0
S4B A:ICS602 4.2 18.8 1.0
CD2 A:TYR216 4.2 21.8 1.0
CE2 A:TYR216 4.4 21.5 1.0
O A:HOH764 4.4 27.4 1.0
NH2 A:ARG347 4.5 22.5 0.5
S3A A:ICS602 4.5 19.7 1.0
S2B A:ICS602 4.5 19.7 1.0
NH1 A:ARG87 4.5 21.9 1.0
O A:HOH833 4.7 25.8 1.0
SG A:CYS262 4.8 20.5 1.0
NE A:ARG347 4.8 29.2 0.5
CG1 A:VAL61 4.8 22.8 1.0
CZ A:ARG347 4.9 28.6 0.5

Iron binding site 4 out of 32 in 5vq3

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Iron binding site 4 out of 32 in the Nitrogenase CP1 at pH 6.5


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Nitrogenase CP1 at pH 6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:20.2
occ:1.00
 FE4 A:ICS602 0.0 20.2 1.0
CX A:ICS602 2.0 19.6 1.0
S3A A:ICS602 2.2 19.7 1.0
S4A A:ICS602 2.3 21.1 1.0
S1A A:ICS602 2.3 21.5 1.0
FE5 A:ICS602 2.6 18.5 1.0
FE1 A:ICS602 2.6 21.1 1.0
FE2 A:ICS602 2.7 19.3 1.0
FE3 A:ICS602 2.7 20.2 1.0
FE7 A:ICS602 3.7 19.4 1.0
FE6 A:ICS602 3.7 18.9 1.0
S2A A:ICS602 3.8 20.7 1.0
N A:GLY345 4.0 19.7 1.0
N A:SER346 4.0 23.2 0.5
CB A:SER346 4.1 25.8 0.5
N A:SER346 4.1 23.3 0.5
CB A:SER346 4.1 25.1 0.5
S4B A:ICS602 4.2 18.8 1.0
S1B A:ICS602 4.2 19.6 1.0
CD A:ARG347 4.3 27.0 0.5
NH1 A:ARG347 4.3 24.7 0.5
S5A A:ICS602 4.5 21.7 1.0
S2B A:ICS602 4.5 19.7 1.0
N A:ARG347 4.6 23.0 0.5
CA A:SER346 4.6 24.7 0.5
CG A:ARG347 4.6 17.5 0.5
C A:GLY345 4.6 26.7 1.0
SG A:CYS262 4.6 20.5 1.0
CA A:GLY345 4.6 24.0 1.0
CA A:SER346 4.6 23.9 0.5
OG A:SER346 4.9 28.4 0.5
CZ A:PHE369 4.9 25.4 1.0
NE A:ARG347 4.9 29.2 0.5
CA A:GLY344 4.9 21.1 1.0
CZ A:ARG347 5.0 26.4 0.5
NE A:ARG347 5.0 34.1 0.5
C A:GLY344 5.0 24.5 1.0

Iron binding site 5 out of 32 in 5vq3

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Iron binding site 5 out of 32 in the Nitrogenase CP1 at pH 6.5


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Nitrogenase CP1 at pH 6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:18.5
occ:1.00
 FE5 A:ICS602 0.0 18.5 1.0
CX A:ICS602 1.9 19.6 1.0
S3A A:ICS602 2.2 19.7 1.0
S4B A:ICS602 2.3 18.8 1.0
S1B A:ICS602 2.3 19.6 1.0
FE4 A:ICS602 2.6 20.2 1.0
FE7 A:ICS602 2.6 19.4 1.0
FE6 A:ICS602 2.6 18.9 1.0
MO1 A:ICS602 2.7 18.5 1.0
ND1 A:HIS482 3.6 22.2 1.0
FE2 A:ICS602 3.7 19.3 1.0
FE3 A:ICS602 3.7 20.2 1.0
S3B A:ICS602 3.8 19.5 1.0
CE1 A:HIS482 4.0 22.0 1.0
NH1 A:ARG347 4.0 24.7 0.5
N A:GLY344 4.2 23.4 1.0
CA A:GLY344 4.2 21.1 1.0
S1A A:ICS602 4.3 21.5 1.0
S4A A:ICS602 4.3 21.1 1.0
S2B A:ICS602 4.5 19.7 1.0
S5A A:ICS602 4.5 21.7 1.0
O7 A:HCA601 4.5 18.1 1.0
CG A:HIS482 4.6 17.0 1.0
O6 A:HCA601 4.7 17.8 1.0
N A:GLY345 4.7 19.7 1.0
CZ A:ARG347 4.9 26.4 0.5
CD A:ARG347 4.9 21.1 0.5
NE A:ARG347 4.9 29.2 0.5
CG A:ARG347 4.9 17.5 0.5
FE1 A:ICS602 5.0 21.1 1.0

Iron binding site 6 out of 32 in 5vq3

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Iron binding site 6 out of 32 in the Nitrogenase CP1 at pH 6.5


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Nitrogenase CP1 at pH 6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:18.9
occ:1.00
 FE6 A:ICS602 0.0 18.9 1.0
CX A:ICS602 2.0 19.6 1.0
S2B A:ICS602 2.2 19.7 1.0
S3B A:ICS602 2.2 19.5 1.0
S1B A:ICS602 2.2 19.6 1.0
FE2 A:ICS602 2.6 19.3 1.0
FE7 A:ICS602 2.6 19.4 1.0
FE5 A:ICS602 2.6 18.5 1.0
MO1 A:ICS602 2.7 18.5 1.0
O7 A:HCA601 3.7 18.1 1.0
FE3 A:ICS602 3.7 20.2 1.0
FE4 A:ICS602 3.7 20.2 1.0
S4B A:ICS602 3.8 18.8 1.0
CZ A:PHE369 4.2 25.4 1.0
S2A A:ICS602 4.3 20.7 1.0
S1A A:ICS602 4.3 21.5 1.0
O2 A:HCA601 4.3 21.1 1.0
S5A A:ICS602 4.4 21.7 1.0
CG2 A:VAL61 4.5 19.5 1.0
S3A A:ICS602 4.5 19.7 1.0
O6 A:HCA601 4.5 17.8 1.0
CE2 A:PHE369 4.6 25.2 1.0
ND1 A:HIS482 4.7 22.2 1.0
C3 A:HCA601 4.8 19.2 1.0
CG1 A:VAL61 4.8 22.8 1.0
C1 A:HCA601 4.9 22.9 1.0
C2 A:HCA601 5.0 21.1 1.0

Iron binding site 7 out of 32 in 5vq3

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Iron binding site 7 out of 32 in the Nitrogenase CP1 at pH 6.5


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Nitrogenase CP1 at pH 6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:19.4
occ:1.00
 FE7 A:ICS602 0.0 19.4 1.0
CX A:ICS602 2.0 19.6 1.0
S5A A:ICS602 2.2 21.7 1.0
S4B A:ICS602 2.2 18.8 1.0
S3B A:ICS602 2.2 19.5 1.0
FE3 A:ICS602 2.6 20.2 1.0
FE6 A:ICS602 2.6 18.9 1.0
FE5 A:ICS602 2.6 18.5 1.0
MO1 A:ICS602 2.7 18.5 1.0
FE2 A:ICS602 3.7 19.3 1.0
FE4 A:ICS602 3.7 20.2 1.0
O6 A:HCA601 3.7 17.8 1.0
O A:HOH797 3.8 20.8 1.0
S1B A:ICS602 3.8 19.6 1.0
NE A:ARG87 4.1 18.9 1.0
S4A A:ICS602 4.3 21.1 1.0
S2A A:ICS602 4.3 20.7 1.0
S2B A:ICS602 4.4 19.7 1.0
S3A A:ICS602 4.5 19.7 1.0
CZ A:ARG347 4.5 28.6 0.5
NH2 A:ARG347 4.5 22.5 0.5
O7 A:HCA601 4.5 18.1 1.0
NH1 A:ARG87 4.6 21.9 1.0
ND1 A:HIS482 4.6 22.2 1.0
NH1 A:ARG347 4.7 19.0 0.5
C7 A:HCA601 4.7 18.7 1.0
NE A:ARG347 4.8 29.2 0.5
CZ A:ARG87 4.8 18.5 1.0
CD A:ARG87 4.9 19.5 1.0

Iron binding site 8 out of 32 in 5vq3

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Iron binding site 8 out of 32 in the Nitrogenase CP1 at pH 6.5


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Nitrogenase CP1 at pH 6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe603

b:18.5
occ:1.00
 FE1 A:CLF603 0.0 18.5 1.0
S3A A:CLF603 2.3 20.2 1.0
S2A A:CLF603 2.3 20.1 1.0
SG A:CYS145 2.3 21.2 1.0
S1 A:CLF603 2.4 19.1 1.0
FE2 A:CLF603 2.5 20.8 1.0
FE4 A:CLF603 2.6 18.6 1.0
FE3 A:CLF603 2.8 18.9 1.0
CB A:CYS145 3.4 21.8 1.0
S4A A:CLF603 3.8 18.6 1.0
N A:CYS145 3.8 19.5 1.0
O B:HOH712 3.9 22.6 1.0
SG B:CYS48 4.0 19.5 1.0
CA A:GLY176 4.1 22.6 1.0
CA A:CYS145 4.2 21.6 1.0
FE8 A:CLF603 4.4 19.8 1.0
N A:GLY176 4.4 21.7 1.0
SG A:CYS79 4.5 19.8 1.0
FE5 A:CLF603 4.6 19.6 1.0
FE6 A:CLF603 4.8 21.0 1.0
CB B:SER45 4.8 21.4 1.0
OG B:SER45 4.9 32.4 1.0
SG A:CYS53 4.9 19.5 1.0
SG B:CYS106 4.9 20.8 1.0
C A:GLY176 5.0 24.5 1.0
C A:THR144 5.0 21.2 1.0

Iron binding site 9 out of 32 in 5vq3

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Iron binding site 9 out of 32 in the Nitrogenase CP1 at pH 6.5


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Nitrogenase CP1 at pH 6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe603

b:20.8
occ:1.00
 FE2 A:CLF603 0.0 20.8 1.0
S2A A:CLF603 2.3 20.1 1.0
S4A A:CLF603 2.3 18.6 1.0
SG B:CYS48 2.3 19.5 1.0
S1 A:CLF603 2.5 19.1 1.0
FE1 A:CLF603 2.5 18.5 1.0
FE4 A:CLF603 2.7 18.6 1.0
FE3 A:CLF603 2.7 18.9 1.0
FE8 A:CLF603 2.9 19.8 1.0
N B:CYS48 3.3 20.5 1.0
CB B:CYS48 3.6 18.4 1.0
CA B:CYS48 3.6 20.9 1.0
S3A A:CLF603 3.8 20.2 1.0
FE5 A:CLF603 3.9 19.6 1.0
C B:GLY47 3.9 21.7 1.0
S4B A:CLF603 4.0 18.8 1.0
O B:HOH712 4.2 22.6 1.0
CA B:GLY47 4.4 19.4 1.0
SG A:CYS145 4.5 21.2 1.0
FE6 A:CLF603 4.6 21.0 1.0
O B:GLY47 4.6 18.2 1.0
O B:SER45 4.7 20.7 1.0
SG A:CYS79 4.7 19.8 1.0
SG A:CYS53 4.8 19.5 1.0
N B:GLY47 4.9 21.0 1.0
S3B A:CLF603 5.0 19.8 1.0

Iron binding site 10 out of 32 in 5vq3

Go back to Iron Binding Sites List in 5vq3
Iron binding site 10 out of 32 in the Nitrogenase CP1 at pH 6.5


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Nitrogenase CP1 at pH 6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe603

b:18.9
occ:1.00
 FE3 A:CLF603 0.0 18.9 1.0
S4A A:CLF603 2.3 18.6 1.0
SG A:CYS53 2.3 19.5 1.0
S2A A:CLF603 2.3 20.1 1.0
S3A A:CLF603 2.3 20.2 1.0
FE4 A:CLF603 2.7 18.6 1.0
FE2 A:CLF603 2.7 20.8 1.0
FE1 A:CLF603 2.8 18.5 1.0
CB A:CYS53 3.3 19.7 1.0
CA A:GLY176 4.0 22.6 1.0
CB A:TYR55 4.1 20.0 1.0
S1 A:CLF603 4.2 19.1 1.0
CA B:GLY47 4.3 19.4 1.0
CD2 A:TYR55 4.3 19.4 1.0
CG A:TYR55 4.6 18.3 1.0
C B:GLY47 4.6 21.7 1.0
N B:CYS48 4.7 20.5 1.0
N A:GLY176 4.7 21.7 1.0
CA A:CYS53 4.8 19.5 1.0
O B:HOH748 4.8 24.3 1.0
SG A:CYS145 4.8 21.2 1.0
N A:TYR55 4.9 17.9 1.0
SG A:CYS79 4.9 19.8 1.0
N B:GLY47 5.0 21.0 1.0
SG B:CYS48 5.0 19.5 1.0
C A:GLY176 5.0 24.5 1.0

Reference:

C.N.Morrison, T.Spatzal, D.C.Rees. Reversible Protonated Resting State of the Nitrogenase Active Site. J. Am. Chem. Soc. V. 139 10856 2017.
ISSN: ESSN 1520-5126
PubMed: 28692802
DOI: 10.1021/JACS.7B05695
Page generated: Tue Aug 6 10:30:45 2024

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