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Iron in PDB 1xcp: Crystal Structure of the Nitrogenase Fe Protein PHE135TRP with Mgadp Bound

Enzymatic activity of Crystal Structure of the Nitrogenase Fe Protein PHE135TRP with Mgadp Bound

All present enzymatic activity of Crystal Structure of the Nitrogenase Fe Protein PHE135TRP with Mgadp Bound:
1.18.6.1;

Protein crystallography data

The structure of Crystal Structure of the Nitrogenase Fe Protein PHE135TRP with Mgadp Bound, PDB code: 1xcp was solved by M.S.Jeong, S.B.Jang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 3.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 108.950, 91.260, 125.310, 90.00, 90.00, 90.00
R / Rfree (%) 22.6 / 32.2

Other elements in 1xcp:

The structure of Crystal Structure of the Nitrogenase Fe Protein PHE135TRP with Mgadp Bound also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of the Nitrogenase Fe Protein PHE135TRP with Mgadp Bound (pdb code 1xcp). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Crystal Structure of the Nitrogenase Fe Protein PHE135TRP with Mgadp Bound, PDB code: 1xcp:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 1xcp

Go back to Iron Binding Sites List in 1xcp
Iron binding site 1 out of 8 in the Crystal Structure of the Nitrogenase Fe Protein PHE135TRP with Mgadp Bound


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 the Nitrogenase Fe Protein PHE135TRP with Mgadp Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1290

b:60.5
occ:1.00
 FE1 B:SF41290 0.0 60.5 1.0
SG B:CYS97 2.1 84.8 1.0
S2 B:SF41290 2.3 50.6 1.0
S4 B:SF41290 2.3 59.4 1.0
S3 B:SF41290 2.4 61.2 1.0
CB B:CYS97 2.5 93.6 1.0
FE4 B:SF41290 2.7 63.9 1.0
FE3 B:SF41290 2.7 62.1 1.0
FE2 B:SF41290 3.0 64.3 1.0
CA B:CYS97 3.1 96.0 1.0
CA B:GLY134 3.8 96.8 1.0
N B:ALA98 3.8 98.6 1.0
C B:CYS97 4.0 96.1 1.0
S1 B:SF41290 4.1 52.9 1.0
N B:CYS97 4.2 98.8 1.0
N B:GLY134 4.5 96.2 1.0
N B:GLY99 4.8 99.6 1.0
C B:GLY134 4.8 97.2 1.0
SG B:CYS132 4.8 98.2 1.0
SG A:CYS132 4.9 98.6 1.0

Iron binding site 2 out of 8 in 1xcp

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Iron binding site 2 out of 8 in the Crystal Structure of the Nitrogenase Fe Protein PHE135TRP with Mgadp Bound


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 the Nitrogenase Fe Protein PHE135TRP with Mgadp Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1290

b:64.3
occ:1.00
 FE2 B:SF41290 0.0 64.3 1.0
S1 B:SF41290 2.3 52.9 1.0
S3 B:SF41290 2.3 61.2 1.0
SG A:CYS97 2.3 88.5 1.0
S4 B:SF41290 2.4 59.4 1.0
CB A:CYS97 2.5 93.4 1.0
FE4 B:SF41290 2.7 63.9 1.0
FE3 B:SF41290 2.7 62.1 1.0
FE1 B:SF41290 3.0 60.5 1.0
CA A:CYS97 3.0 94.1 1.0
N A:ALA98 3.9 95.0 1.0
CA A:GLY134 4.0 98.0 1.0
C A:CYS97 4.0 93.8 1.0
N A:CYS97 4.1 98.5 1.0
S2 B:SF41290 4.1 50.6 1.0
N A:GLY134 4.7 98.6 1.0
SG B:CYS132 4.8 98.2 1.0
C A:GLY96 4.9 0.0 1.0
O A:GLY96 4.9 0.0 1.0

Iron binding site 3 out of 8 in 1xcp

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Iron binding site 3 out of 8 in the Crystal Structure of the Nitrogenase Fe Protein PHE135TRP with Mgadp Bound


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 the Nitrogenase Fe Protein PHE135TRP with Mgadp Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1290

b:62.1
occ:1.00
 FE3 B:SF41290 0.0 62.1 1.0
S4 B:SF41290 2.4 59.4 1.0
S1 B:SF41290 2.4 52.9 1.0
S2 B:SF41290 2.4 50.6 1.0
SG A:CYS132 2.5 98.6 1.0
FE4 B:SF41290 2.5 63.9 1.0
FE1 B:SF41290 2.7 60.5 1.0
FE2 B:SF41290 2.7 64.3 1.0
CB A:CYS132 3.4 98.5 1.0
S3 B:SF41290 3.8 61.2 1.0
CA A:GLY134 3.8 98.0 1.0
N A:GLY134 3.9 98.6 1.0
SG A:CYS97 4.2 88.5 1.0
N A:TRP135 4.3 97.2 1.0
CA B:CYS97 4.5 96.0 1.0
SG B:CYS97 4.5 84.8 1.0
C A:GLY134 4.6 98.0 1.0
CA A:CYS132 4.6 99.0 1.0
CD1 A:TRP135 4.7 90.7 1.0
C A:CYS132 4.7 98.7 1.0
CB B:CYS97 4.7 93.6 1.0
SG B:CYS132 4.8 98.2 1.0
N B:ALA98 4.8 98.6 1.0
N A:GLY133 4.9 98.8 1.0
O B:GLY96 4.9 0.0 1.0

Iron binding site 4 out of 8 in 1xcp

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Iron binding site 4 out of 8 in the Crystal Structure of the Nitrogenase Fe Protein PHE135TRP with Mgadp Bound


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 the Nitrogenase Fe Protein PHE135TRP with Mgadp Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1290

b:63.9
occ:1.00
 FE4 B:SF41290 0.0 63.9 1.0
S3 B:SF41290 2.3 61.2 1.0
S1 B:SF41290 2.3 52.9 1.0
S2 B:SF41290 2.4 50.6 1.0
FE3 B:SF41290 2.5 62.1 1.0
SG B:CYS132 2.5 98.2 1.0
FE2 B:SF41290 2.7 64.3 1.0
FE1 B:SF41290 2.7 60.5 1.0
CB B:CYS132 3.5 99.5 1.0
S4 B:SF41290 3.8 59.4 1.0
CA B:GLY134 4.1 96.8 1.0
N B:GLY134 4.2 96.2 1.0
SG B:CYS97 4.3 84.8 1.0
N B:TRP135 4.5 98.5 1.0
SG A:CYS132 4.5 98.6 1.0
SG A:CYS97 4.5 88.5 1.0
CD1 B:TRP135 4.5 91.7 1.0
CA A:CYS97 4.6 94.1 1.0
C B:GLY134 4.8 97.2 1.0
CA B:CYS132 4.8 99.0 1.0
CB A:CYS97 4.8 93.4 1.0
N A:ALA98 4.9 95.0 1.0
C B:CYS132 4.9 97.2 1.0

Iron binding site 5 out of 8 in 1xcp

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Iron binding site 5 out of 8 in the Crystal Structure of the Nitrogenase Fe Protein PHE135TRP with Mgadp Bound


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 the Nitrogenase Fe Protein PHE135TRP with Mgadp Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe2290

b:51.5
occ:1.00
 FE1 C:SF42290 0.0 51.5 1.0
SG D:CYS97 2.1 70.7 1.0
S2 C:SF42290 2.3 47.8 1.0
S4 C:SF42290 2.3 53.6 1.0
S3 C:SF42290 2.3 51.1 1.0
FE4 C:SF42290 2.7 49.1 1.0
FE3 C:SF42290 2.7 52.2 1.0
FE2 C:SF42290 2.9 48.6 1.0
CB D:CYS97 3.2 78.1 1.0
CA D:CYS97 3.6 78.8 1.0
N D:ALA98 3.7 80.6 1.0
CA D:GLY134 4.0 67.0 1.0
S1 C:SF42290 4.0 41.9 1.0
C D:CYS97 4.1 79.5 1.0
N D:GLY99 4.2 83.1 1.0
N D:GLY134 4.5 67.2 1.0
CA D:ALA98 4.7 82.7 1.0
SG C:CYS97 4.8 69.4 1.0
SG C:CYS132 4.8 59.3 1.0
CB D:ALA98 4.8 83.3 1.0
N D:CYS97 4.9 81.0 1.0
C D:GLY134 5.0 66.7 1.0

Iron binding site 6 out of 8 in 1xcp

Go back to Iron Binding Sites List in 1xcp
Iron binding site 6 out of 8 in the Crystal Structure of the Nitrogenase Fe Protein PHE135TRP with Mgadp Bound


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 the Nitrogenase Fe Protein PHE135TRP with Mgadp Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe2290

b:48.6
occ:1.00
 FE2 C:SF42290 0.0 48.6 1.0
SG C:CYS97 2.0 69.4 1.0
S1 C:SF42290 2.3 41.9 1.0
S3 C:SF42290 2.3 51.1 1.0
S4 C:SF42290 2.4 53.6 1.0
FE4 C:SF42290 2.7 49.1 1.0
FE3 C:SF42290 2.7 52.2 1.0
FE1 C:SF42290 2.9 51.5 1.0
CB C:CYS97 3.0 76.7 1.0
CA C:CYS97 3.5 79.1 1.0
N C:ALA98 3.7 80.4 1.0
CA C:GLY134 4.0 63.2 1.0
C C:CYS97 4.1 79.5 1.0
S2 C:SF42290 4.1 47.8 1.0
N C:GLY99 4.3 83.7 1.0
N C:GLY134 4.5 62.9 1.0
CA C:ALA98 4.8 82.8 1.0
N C:CYS97 4.8 82.6 1.0
SG D:CYS97 4.8 70.7 1.0
SG D:CYS132 4.9 58.3 1.0
CB C:ALA98 4.9 84.6 1.0

Iron binding site 7 out of 8 in 1xcp

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Iron binding site 7 out of 8 in the Crystal Structure of the Nitrogenase Fe Protein PHE135TRP with Mgadp Bound


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 the Nitrogenase Fe Protein PHE135TRP with Mgadp Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe2290

b:52.2
occ:1.00
 FE3 C:SF42290 0.0 52.2 1.0
S4 C:SF42290 2.3 53.6 1.0
S2 C:SF42290 2.3 47.8 1.0
S1 C:SF42290 2.4 41.9 1.0
FE4 C:SF42290 2.5 49.1 1.0
SG C:CYS132 2.6 59.3 1.0
FE1 C:SF42290 2.7 51.5 1.0
FE2 C:SF42290 2.7 48.6 1.0
S3 C:SF42290 3.8 51.1 1.0
CB C:CYS132 3.9 66.1 1.0
N C:GLY134 4.0 62.9 1.0
CA C:GLY134 4.0 63.2 1.0
SG C:CYS97 4.5 69.4 1.0
SG D:CYS132 4.5 58.3 1.0
CD1 C:TRP135 4.6 68.5 1.0
N C:TRP135 4.6 68.5 1.0
SG D:CYS97 4.6 70.7 1.0
N D:ALA98 4.7 80.6 1.0
C C:GLY134 4.8 66.0 1.0
NE1 C:TRP135 4.8 65.4 1.0
CB D:ALA98 5.0 83.3 1.0

Iron binding site 8 out of 8 in 1xcp

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Iron binding site 8 out of 8 in the Crystal Structure of the Nitrogenase Fe Protein PHE135TRP with Mgadp Bound


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 the Nitrogenase Fe Protein PHE135TRP with Mgadp Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe2290

b:49.1
occ:1.00
 FE4 C:SF42290 0.0 49.1 1.0
S3 C:SF42290 2.3 51.1 1.0
S2 C:SF42290 2.3 47.8 1.0
S1 C:SF42290 2.3 41.9 1.0
SG D:CYS132 2.5 58.3 1.0
FE3 C:SF42290 2.5 52.2 1.0
FE1 C:SF42290 2.7 51.5 1.0
FE2 C:SF42290 2.7 48.6 1.0
CB D:CYS132 3.6 63.1 1.0
N D:GLY134 3.7 67.2 1.0
S4 C:SF42290 3.8 53.6 1.0
CA D:GLY134 3.8 67.0 1.0
SG C:CYS97 4.5 69.4 1.0
N D:TRP135 4.5 69.3 1.0
SG D:CYS97 4.5 70.7 1.0
N C:ALA98 4.5 80.4 1.0
C D:GLY134 4.6 66.7 1.0
CD1 D:TRP135 4.7 64.9 1.0
N D:GLY133 4.7 65.7 1.0
CA C:CYS97 4.8 79.1 1.0
CA D:CYS132 4.8 63.8 1.0
C D:CYS132 4.8 65.7 1.0
CB C:ALA98 4.9 84.6 1.0
C D:GLY133 4.9 67.0 1.0
SG C:CYS132 5.0 59.3 1.0

Reference:

M.S.Jeong, S.B.Jang. Structural Basis For the Changes in Redox Potential in the Nitrogenase PHE135TRP Fe Protein with Mgadp Bound Mol.Cell V. 18 374 2004.
ISSN: ISSN 1097-2765
PubMed: 15650336
Page generated: Sat Aug 3 16:52:08 2024

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