Atomistry » Magnesium » PDB 6cfv-6cpt » 6cip
Atomistry »
  Magnesium »
    PDB 6cfv-6cpt »
      6cip »

Magnesium in PDB 6cip: Pyruvate:Ferredoxin Oxidoreductase From Moorella Thermoacetica with Acetyl-Tpp Bound

Protein crystallography data

The structure of Pyruvate:Ferredoxin Oxidoreductase From Moorella Thermoacetica with Acetyl-Tpp Bound, PDB code: 6cip was solved by P.Y.-T.Chen, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 97.45 / 3.19
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 342.005, 108.263, 240.437, 90.00, 109.32, 90.00
R / Rfree (%) 18.7 / 22.5

Other elements in 6cip:

The structure of Pyruvate:Ferredoxin Oxidoreductase From Moorella Thermoacetica with Acetyl-Tpp Bound also contains other interesting chemical elements:

Iron (Fe) 72 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Pyruvate:Ferredoxin Oxidoreductase From Moorella Thermoacetica with Acetyl-Tpp Bound (pdb code 6cip). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Pyruvate:Ferredoxin Oxidoreductase From Moorella Thermoacetica with Acetyl-Tpp Bound, PDB code: 6cip:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 6cip

Go back to Magnesium Binding Sites List in 6cip
Magnesium binding site 1 out of 6 in the Pyruvate:Ferredoxin Oxidoreductase From Moorella Thermoacetica with Acetyl-Tpp Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pyruvate:Ferredoxin Oxidoreductase From Moorella Thermoacetica with Acetyl-Tpp Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1205

b:64.5
occ:1.00
 O23 A:HTL1204 2.1 0.6 1.0
OD1 A:ASP967 2.1 0.2 1.0
O A:HOH1301 2.1 63.7 1.0
O13 A:HTL1204 2.2 0.3 1.0
OG1 A:THR995 2.2 0.6 1.0
O A:VAL997 2.2 94.0 1.0
P2 A:HTL1204 3.2 0.7 1.0
CG A:ASP967 3.3 0.8 1.0
P1 A:HTL1204 3.3 97.2 1.0
C A:VAL997 3.5 100.0 1.0
O11 A:HTL1204 3.5 0.8 1.0
CB A:THR995 3.6 92.2 1.0
OG A:SER999 3.7 0.9 1.0
N A:SER999 3.9 0.1 1.0
OD2 A:ASP967 3.9 0.6 1.0
N A:ASP967 3.9 98.7 1.0
O21 A:HTL1204 3.9 99.4 1.0
N A:THR995 4.0 97.7 1.0
O5G A:HTL1204 4.1 95.8 1.0
CG2 A:THR995 4.1 85.5 1.0
N A:VAL997 4.2 0.5 1.0
CA A:THR995 4.2 98.8 1.0
CA A:TYR998 4.3 0.7 1.0
N A:TYR998 4.3 0.1 1.0
CB A:SER999 4.3 0.9 1.0
CB A:ASP967 4.4 0.6 1.0
O A:LEU993 4.4 97.1 1.0
N A:GLY968 4.4 98.9 1.0
O22 A:HTL1204 4.4 0.5 1.0
CA A:VAL997 4.5 0.9 1.0
O12 A:HTL1204 4.5 94.3 1.0
C A:THR995 4.5 95.7 1.0
N A:GLU996 4.6 99.4 1.0
CA A:ASP967 4.6 0.1 1.0
C A:TYR998 4.6 0.8 1.0
CA A:GLY966 4.7 69.6 1.0
CA A:SER999 4.8 0.5 1.0
C A:GLY966 4.8 99.0 1.0
OE2 A:GLU814 4.8 0.8 1.0
CG2 A:VAL997 5.0 0.1 1.0

Magnesium binding site 2 out of 6 in 6cip

Go back to Magnesium Binding Sites List in 6cip
Magnesium binding site 2 out of 6 in the Pyruvate:Ferredoxin Oxidoreductase From Moorella Thermoacetica with Acetyl-Tpp Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Pyruvate:Ferredoxin Oxidoreductase From Moorella Thermoacetica with Acetyl-Tpp Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1205

b:66.6
occ:1.00
 O B:HOH1302 1.8 75.7 1.0
OD1 B:ASP967 2.0 0.4 1.0
O B:VAL997 2.0 0.0 1.0
O12 B:HTL1204 2.1 0.6 1.0
O21 B:HTL1204 2.2 0.1 1.0
OG1 B:THR995 2.2 0.8 1.0
CG B:ASP967 3.2 0.1 1.0
P1 B:HTL1204 3.2 0.1 1.0
P2 B:HTL1204 3.3 0.5 1.0
C B:VAL997 3.3 0.7 1.0
O11 B:HTL1204 3.4 0.8 1.0
CB B:THR995 3.6 0.3 1.0
N B:ASP967 3.8 0.3 1.0
OD2 B:ASP967 3.8 0.3 1.0
N B:SER999 3.9 0.6 1.0
O22 B:HTL1204 3.9 0.2 1.0
O5G B:HTL1204 3.9 0.2 1.0
N B:VAL997 4.0 0.9 1.0
N B:THR995 4.0 0.7 1.0
CA B:TYR998 4.1 0.2 1.0
N B:TYR998 4.1 0.4 1.0
CG2 B:THR995 4.1 0.5 1.0
OG B:SER999 4.1 97.1 1.0
CA B:THR995 4.2 0.5 1.0
CB B:ASP967 4.2 0.9 1.0
CA B:VAL997 4.3 0.1 1.0
N B:GLY968 4.3 97.5 1.0
O13 B:HTL1204 4.4 0.6 1.0
C B:THR995 4.5 0.5 1.0
O23 B:HTL1204 4.5 0.2 1.0
CA B:ASP967 4.5 0.7 1.0
O B:LEU993 4.5 91.0 1.0
C B:TYR998 4.5 0.2 1.0
N B:GLU996 4.6 0.1 1.0
CA B:GLY966 4.6 0.2 1.0
CB B:SER999 4.6 99.5 1.0
C B:GLY966 4.7 0.1 1.0
CA B:SER999 4.9 0.7 1.0
C B:ASP967 4.9 0.6 1.0
CG2 B:VAL997 5.0 0.3 1.0

Magnesium binding site 3 out of 6 in 6cip

Go back to Magnesium Binding Sites List in 6cip
Magnesium binding site 3 out of 6 in the Pyruvate:Ferredoxin Oxidoreductase From Moorella Thermoacetica with Acetyl-Tpp Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Pyruvate:Ferredoxin Oxidoreductase From Moorella Thermoacetica with Acetyl-Tpp Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1205

b:49.0
occ:1.00
 O C:VAL997 1.9 1.0 1.0
O C:HOH1303 2.0 53.4 1.0
O13 C:HTL1204 2.1 96.5 1.0
OD1 C:ASP967 2.1 0.3 1.0
OG1 C:THR995 2.1 0.8 1.0
O23 C:HTL1204 2.4 86.1 1.0
C C:VAL997 3.1 98.3 1.0
P1 C:HTL1204 3.2 85.0 1.0
CG C:ASP967 3.2 0.1 1.0
P2 C:HTL1204 3.4 85.8 1.0
O11 C:HTL1204 3.4 84.5 1.0
CB C:THR995 3.5 0.0 1.0
N C:SER999 3.8 96.8 1.0
OD2 C:ASP967 3.9 0.6 1.0
N C:VAL997 3.9 0.1 1.0
N C:TYR998 3.9 98.0 1.0
O5G C:HTL1204 4.0 89.0 1.0
CA C:TYR998 4.0 97.6 1.0
O22 C:HTL1204 4.0 84.0 1.0
CG2 C:THR995 4.1 97.9 1.0
OG C:SER999 4.1 88.0 1.0
N C:ASP967 4.1 95.7 1.0
N C:THR995 4.2 0.6 1.0
CA C:VAL997 4.2 99.9 1.0
CA C:THR995 4.3 0.1 1.0
CB C:ASP967 4.4 92.2 1.0
O12 C:HTL1204 4.4 87.6 1.0
C C:TYR998 4.4 98.6 1.0
C C:THR995 4.5 0.2 1.0
N C:GLY968 4.5 78.5 1.0
N C:GLU996 4.6 0.0 1.0
CB C:SER999 4.6 92.2 1.0
O21 C:HTL1204 4.7 81.8 1.0
O C:LEU993 4.8 89.6 1.0
CA C:ASP967 4.8 87.6 1.0
CA C:SER999 4.8 97.4 1.0
CG2 C:VAL997 4.9 91.5 1.0
CD1 C:TYR998 5.0 94.2 1.0
CA C:GLY966 5.0 0.5 1.0

Magnesium binding site 4 out of 6 in 6cip

Go back to Magnesium Binding Sites List in 6cip
Magnesium binding site 4 out of 6 in the Pyruvate:Ferredoxin Oxidoreductase From Moorella Thermoacetica with Acetyl-Tpp Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Pyruvate:Ferredoxin Oxidoreductase From Moorella Thermoacetica with Acetyl-Tpp Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1205

b:36.6
occ:1.00
 OD1 D:ASP967 2.0 95.1 1.0
O13 D:HTL1204 2.1 90.8 1.0
O23 D:HTL1204 2.1 91.4 1.0
O D:HOH1301 2.2 40.5 1.0
O D:VAL997 2.2 76.2 1.0
OG1 D:THR995 2.4 73.7 1.0
CG D:ASP967 3.1 88.7 1.0
P1 D:HTL1204 3.2 79.9 1.0
P2 D:HTL1204 3.2 82.3 1.0
O11 D:HTL1204 3.4 82.8 1.0
C D:VAL997 3.5 82.2 1.0
CB D:THR995 3.7 74.9 1.0
OD2 D:ASP967 3.7 89.2 1.0
N D:ASP967 3.8 80.4 1.0
O22 D:HTL1204 3.9 74.2 1.0
N D:SER999 3.9 0.2 1.0
OG D:SER999 3.9 0.7 1.0
O5G D:HTL1204 4.0 79.9 1.0
N D:THR995 4.0 81.6 1.0
CG2 D:THR995 4.1 83.3 1.0
CB D:ASP967 4.2 84.4 1.0
N D:VAL997 4.2 86.0 1.0
N D:GLY968 4.2 73.1 1.0
CA D:TYR998 4.2 92.1 1.0
O D:LEU993 4.3 74.7 1.0
N D:TYR998 4.3 88.0 1.0
CA D:THR995 4.3 81.5 1.0
O12 D:HTL1204 4.4 81.9 1.0
CA D:ASP967 4.4 81.0 1.0
CB D:SER999 4.5 0.9 1.0
CA D:VAL997 4.5 83.1 1.0
O21 D:HTL1204 4.5 84.4 1.0
CA D:GLY966 4.6 67.6 1.0
C D:TYR998 4.6 94.0 1.0
C D:THR995 4.6 77.2 1.0
C D:GLY966 4.6 68.3 1.0
N D:GLU996 4.7 77.3 1.0
CA D:SER999 4.8 0.1 1.0
C D:ASP967 4.8 76.1 1.0

Magnesium binding site 5 out of 6 in 6cip

Go back to Magnesium Binding Sites List in 6cip
Magnesium binding site 5 out of 6 in the Pyruvate:Ferredoxin Oxidoreductase From Moorella Thermoacetica with Acetyl-Tpp Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Pyruvate:Ferredoxin Oxidoreductase From Moorella Thermoacetica with Acetyl-Tpp Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1205

b:43.7
occ:1.00
 OG1 E:THR995 2.0 83.6 1.0
O E:HOH1306 2.0 50.9 1.0
O21 E:HTL1204 2.1 86.6 1.0
O E:VAL997 2.1 0.4 1.0
OD1 E:ASP967 2.2 95.2 1.0
O12 E:HTL1204 2.2 84.4 1.0
P2 E:HTL1204 3.3 78.7 1.0
CG E:ASP967 3.3 88.7 1.0
C E:VAL997 3.3 0.5 1.0
P1 E:HTL1204 3.4 75.1 1.0
CB E:THR995 3.4 73.9 1.0
O11 E:HTL1204 3.5 77.5 1.0
OG E:SER999 3.8 0.1 1.0
N E:SER999 3.9 0.6 1.0
O22 E:HTL1204 3.9 74.3 1.0
N E:ASP967 3.9 72.3 1.0
OD2 E:ASP967 3.9 92.8 1.0
N E:THR995 4.0 73.4 1.0
CG2 E:THR995 4.0 65.8 1.0
N E:VAL997 4.0 89.7 1.0
CA E:THR995 4.1 76.5 1.0
O5G E:HTL1204 4.1 76.4 1.0
N E:TYR998 4.2 0.0 1.0
CA E:TYR998 4.2 0.3 1.0
CA E:VAL997 4.3 97.5 1.0
C E:THR995 4.4 74.3 1.0
CB E:ASP967 4.4 80.5 1.0
CB E:SER999 4.4 0.2 1.0
N E:GLY968 4.4 68.9 1.0
N E:GLU996 4.5 75.0 1.0
O23 E:HTL1204 4.5 88.2 1.0
O13 E:HTL1204 4.5 80.1 1.0
O E:LEU993 4.5 66.6 1.0
C E:TYR998 4.6 0.8 1.0
CA E:ASP967 4.6 74.7 1.0
CA E:GLY966 4.7 64.5 1.0
CA E:SER999 4.8 0.5 1.0
C E:GLY966 4.8 65.3 1.0
OE2 E:GLU814 4.8 66.1 1.0
CG2 E:VAL997 5.0 0.7 1.0
O E:THR995 5.0 76.7 1.0

Magnesium binding site 6 out of 6 in 6cip

Go back to Magnesium Binding Sites List in 6cip
Magnesium binding site 6 out of 6 in the Pyruvate:Ferredoxin Oxidoreductase From Moorella Thermoacetica with Acetyl-Tpp Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Pyruvate:Ferredoxin Oxidoreductase From Moorella Thermoacetica with Acetyl-Tpp Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg1205

b:33.5
occ:1.00
 O F:HOH1303 1.9 34.1 1.0
O12 F:HTL1204 2.0 76.1 1.0
OD1 F:ASP967 2.1 81.3 1.0
O F:VAL997 2.1 84.2 1.0
O23 F:HTL1204 2.2 75.8 1.0
OG1 F:THR995 2.4 78.9 1.0
P1 F:HTL1204 3.1 71.7 1.0
CG F:ASP967 3.1 76.0 1.0
P2 F:HTL1204 3.2 68.4 1.0
O11 F:HTL1204 3.2 72.6 1.0
C F:VAL997 3.4 80.7 1.0
OD2 F:ASP967 3.6 79.7 1.0
CB F:THR995 3.7 76.8 1.0
O21 F:HTL1204 3.8 54.8 1.0
N F:SER999 3.9 0.3 1.0
N F:ASP967 3.9 63.9 1.0
O5G F:HTL1204 3.9 74.0 1.0
CA F:TYR998 4.1 89.0 1.0
OG F:SER999 4.1 0.0 1.0
N F:THR995 4.1 74.0 1.0
N F:TYR998 4.2 82.0 1.0
CG2 F:THR995 4.2 74.5 1.0
N F:VAL997 4.2 73.8 1.0
N F:GLY968 4.2 54.0 1.0
O13 F:HTL1204 4.3 69.6 1.0
CB F:ASP967 4.3 68.2 1.0
CA F:THR995 4.4 76.0 1.0
CA F:VAL997 4.4 78.1 1.0
O22 F:HTL1204 4.5 70.5 1.0
O F:LEU993 4.5 59.0 1.0
C F:TYR998 4.5 96.0 1.0
CA F:ASP967 4.5 63.9 1.0
CB F:SER999 4.6 0.8 1.0
CA F:GLY966 4.7 59.4 1.0
C F:THR995 4.7 73.6 1.0
C F:GLY966 4.7 57.3 1.0
N F:GLU996 4.8 73.4 1.0
CA F:SER999 4.9 0.6 1.0
C F:ASP967 4.9 58.7 1.0

Reference:

P.Y.Chen, H.Aman, M.Can, S.W.Ragsdale, C.L.Drennan. Binding Site For Coenzyme A Revealed in the Structure of Pyruvate:Ferredoxin Oxidoreductase Frommoorella Thermoacetica. Proc. Natl. Acad. Sci. V. 115 3846 2018U.S.A..
ISSN: ESSN 1091-6490
PubMed: 29581263
DOI: 10.1073/PNAS.1722329115
Page generated: Mon Sep 30 22:21:37 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy