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Iron in PDB 4s23: Structure of the Gcpe-Hmbpp Complex From Thermus Thermophilius

Enzymatic activity of Structure of the Gcpe-Hmbpp Complex From Thermus Thermophilius

All present enzymatic activity of Structure of the Gcpe-Hmbpp Complex From Thermus Thermophilius:
1.17.7.1;

Protein crystallography data

The structure of Structure of the Gcpe-Hmbpp Complex From Thermus Thermophilius, PDB code: 4s23 was solved by I.Rekittke, E.Warkentin, H.Jomaa, E.Ermler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.95 / 1.65
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 63.250, 63.250, 372.120, 90.00, 90.00, 120.00
R / Rfree (%) 12 / 17

Iron Binding Sites:

The binding sites of Iron atom in the Structure of the Gcpe-Hmbpp Complex From Thermus Thermophilius (pdb code 4s23). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Structure of the Gcpe-Hmbpp Complex From Thermus Thermophilius, PDB code: 4s23:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 4s23

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Iron binding site 1 out of 8 in the Structure of the Gcpe-Hmbpp Complex From Thermus Thermophilius


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of the Gcpe-Hmbpp Complex From Thermus Thermophilius within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:12.2
occ:1.00
 FE1 A:SF4501 0.0 12.2 1.0
S4 A:SF4501 2.2 11.8 1.0
S3 A:SF4501 2.2 18.6 1.0
S2 A:SF4501 2.3 14.2 1.0
SG A:CYS300 2.5 11.4 1.0
FE2 A:SF4501 2.6 12.8 1.0
FE3 A:SF4501 2.7 13.9 1.0
FE4 A:SF4501 2.7 13.2 1.0
CB A:CYS300 3.3 11.6 1.0
N A:CYS300 3.5 14.1 1.0
S1 A:SF4501 3.9 18.2 1.0
CA A:CYS300 4.0 12.1 1.0
C A:GLY299 4.1 11.3 1.0
C21 B:H6P503 4.1 15.9 1.0
CA A:GLY299 4.5 9.9 1.0
CB A:ARG302 4.6 9.3 1.0
SG A:CYS343 4.6 9.7 1.0
C A:CYS300 4.7 9.5 1.0
O B:HOH610 4.7 10.5 1.0
O A:GLY299 4.8 10.2 1.0
O B:HOH602 4.8 15.7 1.0
CD A:ARG302 4.8 7.8 1.0
C30 B:H6P503 4.9 16.8 1.0
CG A:ARG302 4.9 8.4 1.0
N A:GLY299 5.0 10.1 1.0
SG A:CYS297 5.0 9.1 1.0

Iron binding site 2 out of 8 in 4s23

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Iron binding site 2 out of 8 in the Structure of the Gcpe-Hmbpp Complex From Thermus Thermophilius


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of the Gcpe-Hmbpp Complex From Thermus Thermophilius within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:12.8
occ:1.00
 FE2 A:SF4501 0.0 12.8 1.0
S3 A:SF4501 2.3 18.6 1.0
S1 A:SF4501 2.3 18.2 1.0
S4 A:SF4501 2.3 11.8 1.0
SG A:CYS343 2.4 9.7 1.0
FE3 A:SF4501 2.6 13.9 1.0
FE1 A:SF4501 2.6 12.2 1.0
FE4 A:SF4501 2.6 13.2 1.0
CB A:CYS343 3.3 11.9 1.0
N A:CYS343 3.5 12.1 1.0
S2 A:SF4501 3.8 14.2 1.0
CA A:CYS343 3.8 11.4 1.0
C A:GLY342 4.2 7.9 1.0
C A:CYS343 4.2 11.5 1.0
O A:CYS343 4.3 11.1 1.0
CB A:VAL345 4.6 12.4 1.0
CA A:GLY342 4.6 7.7 1.0
CB A:ARG302 4.6 9.3 1.0
SG A:CYS300 4.6 11.4 1.0
O A:HOH852 4.7 11.5 1.0
CD A:ARG302 4.8 7.8 1.0
N A:GLY342 4.8 10.8 1.0
O A:GLY342 4.8 10.4 1.0
NE A:ARG302 4.9 13.0 1.0
N A:VAL345 4.9 14.9 1.0
SG A:CYS297 4.9 9.1 1.0
CG2 A:VAL345 5.0 10.1 1.0

Iron binding site 3 out of 8 in 4s23

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Iron binding site 3 out of 8 in the Structure of the Gcpe-Hmbpp Complex From Thermus Thermophilius


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of the Gcpe-Hmbpp Complex From Thermus Thermophilius within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:13.9
occ:1.00
 FE3 A:SF4501 0.0 13.9 1.0
S1 A:SF4501 2.2 18.2 1.0
S2 A:SF4501 2.2 14.2 1.0
S4 A:SF4501 2.3 11.8 1.0
SG A:CYS297 2.5 9.1 1.0
FE4 A:SF4501 2.5 13.2 1.0
FE2 A:SF4501 2.6 12.8 1.0
FE1 A:SF4501 2.7 12.2 1.0
CB A:CYS297 3.2 8.8 1.0
S3 A:SF4501 3.8 18.6 1.0
N A:GLY342 3.9 10.8 1.0
CA A:GLY299 3.9 9.9 1.0
N A:GLY299 4.0 10.1 1.0
CA A:GLY342 4.0 7.7 1.0
O A:HOH852 4.3 11.5 1.0
N A:CYS343 4.4 12.1 1.0
N A:CYS300 4.5 14.1 1.0
C A:GLY299 4.5 11.3 1.0
C A:GLY342 4.5 7.9 1.0
CA A:CYS297 4.6 6.6 1.0
SG A:CYS343 4.9 9.7 1.0
C A:CYS297 5.0 9.5 1.0
N A:PRO298 5.0 7.7 1.0
CD A:PRO298 5.0 10.8 1.0

Iron binding site 4 out of 8 in 4s23

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Iron binding site 4 out of 8 in the Structure of the Gcpe-Hmbpp Complex From Thermus Thermophilius


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of the Gcpe-Hmbpp Complex From Thermus Thermophilius within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:13.2
occ:1.00
 FE4 A:SF4501 0.0 13.2 1.0
S3 A:SF4501 2.2 18.6 1.0
S1 A:SF4501 2.2 18.2 1.0
S2 A:SF4501 2.3 14.2 1.0
O A:HOH852 2.4 11.5 1.0
FE3 A:SF4501 2.5 13.9 1.0
FE2 A:SF4501 2.6 12.8 1.0
FE1 A:SF4501 2.7 12.2 1.0
C30 B:H6P503 3.6 16.8 1.0
C21 B:H6P503 3.7 15.9 1.0
S4 A:SF4501 3.8 11.8 1.0
C27 B:H6P503 3.9 16.9 1.0
ND2 A:ASN346 4.0 10.9 1.0
C31 B:H6P503 4.1 15.8 1.0
CB A:CYS297 4.4 8.8 1.0
C28 B:H6P503 4.4 14.8 1.0
SG A:CYS297 4.6 9.1 1.0
OE2 B:GLU232 4.7 6.4 1.0
CB A:ASN346 4.7 7.5 1.0
SG A:CYS343 4.7 9.7 1.0
CG A:ASN346 4.9 6.8 1.0
SG A:CYS300 5.0 11.4 1.0
CE A:MET341 5.0 6.9 1.0

Iron binding site 5 out of 8 in 4s23

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Iron binding site 5 out of 8 in the Structure of the Gcpe-Hmbpp Complex From Thermus Thermophilius


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structure of the Gcpe-Hmbpp Complex From Thermus Thermophilius within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:11.1
occ:1.00
 FE1 B:SF4501 0.0 11.1 1.0
S4 B:SF4501 2.2 11.7 1.0
S3 B:SF4501 2.3 18.4 1.0
S2 B:SF4501 2.3 14.9 1.0
SG B:CYS300 2.5 10.6 1.0
FE2 B:SF4501 2.6 11.6 1.0
FE3 B:SF4501 2.7 11.3 1.0
FE4 B:SF4501 2.7 13.3 1.0
CB B:CYS300 3.4 8.5 1.0
N B:CYS300 3.6 8.0 1.0
O B:HOH912 3.8 31.0 1.0
S1 B:SF4501 3.8 17.1 1.0
CA B:CYS300 4.0 10.4 1.0
C21 A:H6P503 4.2 10.0 1.0
C B:GLY299 4.2 11.9 1.0
CB B:ARG302 4.4 14.4 1.0
O A:HOH606 4.5 12.4 1.0
SG B:CYS343 4.6 11.4 1.0
CD B:ARG302 4.6 8.1 1.0
CA B:GLY299 4.7 11.3 1.0
C B:CYS300 4.7 8.9 1.0
CG B:ARG302 4.8 8.1 1.0
O B:GLY299 5.0 10.2 1.0
O A:HOH607 5.0 16.4 1.0
O B:CYS300 5.0 10.8 1.0
O A:HOH1120 5.0 7.6 1.0

Iron binding site 6 out of 8 in 4s23

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Iron binding site 6 out of 8 in the Structure of the Gcpe-Hmbpp Complex From Thermus Thermophilius


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Structure of the Gcpe-Hmbpp Complex From Thermus Thermophilius within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:11.6
occ:1.00
 FE2 B:SF4501 0.0 11.6 1.0
S3 B:SF4501 2.2 18.4 1.0
S1 B:SF4501 2.2 17.1 1.0
S4 B:SF4501 2.3 11.7 1.0
SG B:CYS343 2.5 11.4 1.0
FE1 B:SF4501 2.6 11.1 1.0
FE3 B:SF4501 2.6 11.3 1.0
FE4 B:SF4501 2.6 13.3 1.0
CB B:CYS343 3.4 8.1 1.0
N B:CYS343 3.6 9.1 1.0
S2 B:SF4501 3.8 14.9 1.0
CA B:CYS343 3.9 8.1 1.0
C B:GLY342 4.2 11.9 1.0
C B:CYS343 4.3 8.2 1.0
O B:CYS343 4.4 8.0 1.0
CB B:VAL345 4.4 7.9 1.0
CB B:ARG302 4.6 14.4 1.0
CA B:GLY342 4.6 10.4 1.0
SG B:CYS300 4.7 10.6 1.0
CD B:ARG302 4.7 8.1 1.0
O A:HOH607 4.8 16.4 1.0
CG2 B:VAL345 4.8 8.5 1.0
N B:GLY342 4.8 9.8 1.0
N B:VAL345 4.8 9.3 1.0
O B:GLY342 4.8 8.1 1.0
NE B:ARG302 4.8 8.2 1.0
O B:HOH912 4.9 31.0 1.0
SG B:CYS297 4.9 10.8 1.0

Iron binding site 7 out of 8 in 4s23

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Iron binding site 7 out of 8 in the Structure of the Gcpe-Hmbpp Complex From Thermus Thermophilius


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Structure of the Gcpe-Hmbpp Complex From Thermus Thermophilius within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:11.3
occ:1.00
 FE3 B:SF4501 0.0 11.3 1.0
S4 B:SF4501 2.2 11.7 1.0
S1 B:SF4501 2.3 17.1 1.0
S2 B:SF4501 2.3 14.9 1.0
O B:HOH912 2.5 31.0 1.0
SG B:CYS297 2.5 10.8 1.0
FE4 B:SF4501 2.6 13.3 1.0
FE2 B:SF4501 2.6 11.6 1.0
FE1 B:SF4501 2.7 11.1 1.0
CB B:CYS297 3.3 7.7 1.0
S3 B:SF4501 3.8 18.4 1.0
N B:GLY342 3.9 9.8 1.0
N B:GLY299 4.0 13.1 1.0
CA B:GLY342 4.0 10.4 1.0
CA B:GLY299 4.0 11.3 1.0
O A:HOH607 4.2 16.4 1.0
N B:CYS343 4.4 9.1 1.0
N B:CYS300 4.5 8.0 1.0
C B:GLY342 4.5 11.9 1.0
C B:GLY299 4.5 11.9 1.0
CA B:CYS297 4.6 7.0 1.0
C B:CYS297 4.9 10.8 1.0
N B:PRO298 4.9 11.2 1.0
CG2 B:THR303 5.0 10.1 1.0
SG B:CYS343 5.0 11.4 1.0

Iron binding site 8 out of 8 in 4s23

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Iron binding site 8 out of 8 in the Structure of the Gcpe-Hmbpp Complex From Thermus Thermophilius


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Structure of the Gcpe-Hmbpp Complex From Thermus Thermophilius within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:13.3
occ:1.00
 FE4 B:SF4501 0.0 13.3 1.0
S2 B:SF4501 2.2 14.9 1.0
S1 B:SF4501 2.3 17.1 1.0
S3 B:SF4501 2.3 18.4 1.0
O A:HOH607 2.4 16.4 1.0
FE3 B:SF4501 2.6 11.3 1.0
FE2 B:SF4501 2.6 11.6 1.0
FE1 B:SF4501 2.7 11.1 1.0
C30 A:H6P503 3.8 9.9 1.0
S4 B:SF4501 3.8 11.7 1.0
C21 A:H6P503 3.8 10.0 1.0
O B:HOH912 3.9 31.0 1.0
C27 A:H6P503 3.9 8.4 1.0
C28 A:H6P503 4.2 12.8 1.0
ND2 B:ASN346 4.2 7.9 1.0
CB B:CYS297 4.3 7.7 1.0
OE2 A:GLU232 4.5 14.1 1.0
C31 A:H6P503 4.5 14.8 1.0
SG B:CYS297 4.5 10.8 1.0
CB B:ASN346 4.7 7.5 1.0
SG B:CYS343 4.8 11.4 1.0
CB B:VAL345 4.9 7.9 1.0
N B:ASN346 4.9 7.8 1.0
O29 A:H6P503 5.0 9.8 1.0
SG B:CYS300 5.0 10.6 1.0

Reference:

I.Rekittke, E.Warkentin, H.Jomaa, U.Ermler. Structure of the Gcpe-Hmbpp Complex From Thermus Thermophilius. Biochem.Biophys.Res.Commun. V. 458 246 2015.
ISSN: ISSN 0006-291X
PubMed: 25660452
DOI: 10.1016/J.BBRC.2015.01.088
Page generated: Tue Aug 5 14:28:55 2025

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