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Manganese in PDB 2fah: The Structure of Mitochondrial Pepck, Complex with Mn and Gdp

Enzymatic activity of The Structure of Mitochondrial Pepck, Complex with Mn and Gdp

All present enzymatic activity of The Structure of Mitochondrial Pepck, Complex with Mn and Gdp:
4.1.1.32;

Protein crystallography data

The structure of The Structure of Mitochondrial Pepck, Complex with Mn and Gdp, PDB code: 2fah was solved by T.Holyoak, S.M.Sullivan, T.Nowak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.81 / 2.09
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 74.595, 90.852, 103.339, 64.23, 73.74, 71.18
R / Rfree (%) 18.7 / 23.4

Manganese Binding Sites:

The binding sites of Manganese atom in the The Structure of Mitochondrial Pepck, Complex with Mn and Gdp (pdb code 2fah). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the The Structure of Mitochondrial Pepck, Complex with Mn and Gdp, PDB code: 2fah:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 2fah

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Manganese binding site 1 out of 8 in the The Structure of Mitochondrial Pepck, Complex with Mn and Gdp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of The Structure of Mitochondrial Pepck, Complex with Mn and Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn2002

b:15.3
occ:0.60
 O A:HOH2138 2.0 15.9 1.0
OD1 A:ASP330 2.0 16.4 1.0
NZ A:LYS263 2.1 16.2 1.0
NE2 A:HIS283 2.3 14.7 1.0
O1B A:MLA2001 2.6 36.0 1.0
CG A:ASP330 3.1 15.5 1.0
CD2 A:HIS283 3.2 14.8 1.0
CE1 A:HIS283 3.3 15.0 1.0
CE A:LYS263 3.3 15.4 1.0
OD2 A:ASP330 3.4 16.0 1.0
C1 A:MLA2001 3.7 36.0 1.0
OG A:SER305 3.8 17.9 1.0
CE A:LYS309 3.9 13.1 1.0
O A:HOH2141 3.9 18.2 1.0
NZ A:LYS309 3.9 12.5 1.0
O A:HOH2139 4.0 26.2 1.0
O1A A:MLA2001 4.2 34.1 1.0
O A:HOH2203 4.2 23.4 1.0
ND1 A:HIS283 4.4 15.2 1.0
CB A:ASP330 4.4 15.0 1.0
CG A:HIS283 4.4 15.0 1.0
CB A:SER305 4.5 15.5 1.0
CA A:SER305 4.6 15.9 1.0
CD A:LYS263 4.6 14.6 1.0
C2 A:MLA2001 4.8 36.1 1.0
CA A:ASP330 4.8 15.1 1.0
O A:ASP330 5.0 15.0 1.0

Manganese binding site 2 out of 8 in 2fah

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Manganese binding site 2 out of 8 in the The Structure of Mitochondrial Pepck, Complex with Mn and Gdp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of The Structure of Mitochondrial Pepck, Complex with Mn and Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn2003

b:21.9
occ:0.30
 O2A A:GDP2000 2.6 12.0 1.0
N A:VAL354 2.9 14.4 1.0
O1B A:GDP2000 2.9 13.7 1.0
OG1 A:THR310 3.1 15.4 1.0
O2B A:GDP2000 3.1 14.1 1.0
CA A:GLY353 3.2 14.8 1.0
PB A:GDP2000 3.4 15.1 1.0
C A:GLY353 3.6 14.7 1.0
O A:HOH2050 3.6 9.4 1.0
O A:HOH2139 3.8 26.2 1.0
CG2 A:VAL354 3.8 14.4 1.0
PA A:GDP2000 3.8 13.4 1.0
O3A A:GDP2000 3.9 14.3 1.0
CB A:VAL354 3.9 14.8 1.0
NH1 A:ARG424 3.9 15.5 1.0
CB A:THR310 3.9 15.1 1.0
O A:HOH2141 3.9 18.2 1.0
O A:PHE352 4.0 15.3 1.0
CA A:VAL354 4.0 14.7 1.0
N A:GLY353 4.4 14.8 1.0
O A:HOH2203 4.5 23.4 1.0
C A:PHE352 4.6 15.1 1.0
O1A A:GDP2000 4.7 11.0 1.0
CG2 A:THR310 4.7 14.9 1.0
OD2 A:ASP329 4.8 18.9 1.0
O A:GLY353 4.8 14.8 1.0
CZ A:ARG424 4.8 15.7 1.0
O3B A:GDP2000 4.9 10.8 1.0
O A:VAL354 4.9 14.9 1.0
O5' A:GDP2000 5.0 13.5 1.0
C A:VAL354 5.0 15.2 1.0

Manganese binding site 3 out of 8 in 2fah

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Manganese binding site 3 out of 8 in the The Structure of Mitochondrial Pepck, Complex with Mn and Gdp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of The Structure of Mitochondrial Pepck, Complex with Mn and Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn3002

b:28.4
occ:0.50
 O B:HOH6054 1.9 20.1 1.0
NZ B:LYS263 2.0 16.8 1.0
OD1 B:ASP330 2.2 16.4 1.0
NE2 B:HIS283 2.3 15.0 1.0
O3A B:MLA3001 2.6 29.8 1.0
CE B:LYS263 3.1 15.4 1.0
CG B:ASP330 3.1 15.4 1.0
CD2 B:HIS283 3.2 15.0 1.0
CE1 B:HIS283 3.3 15.1 1.0
OD2 B:ASP330 3.5 15.7 1.0
OG B:SER305 3.7 17.2 1.0
C3 B:MLA3001 3.7 28.1 1.0
CE B:LYS309 4.1 16.1 1.0
NZ B:LYS309 4.2 19.0 1.0
O B:HOH6037 4.3 16.9 1.0
O B:HOH6100 4.3 20.8 1.0
ND1 B:HIS283 4.4 15.4 1.0
O3B B:MLA3001 4.4 27.6 1.0
CG B:HIS283 4.4 15.1 1.0
CD B:LYS263 4.4 14.7 1.0
O B:HOH6218 4.4 31.3 1.0
CB B:SER305 4.5 15.6 1.0
CB B:ASP330 4.5 15.1 1.0
CA B:SER305 4.6 15.8 1.0
C2 B:MLA3001 4.7 27.9 1.0
CZ B:PHE504 4.8 14.1 1.0
CE2 B:PHE504 4.9 14.7 1.0
O1B B:MLA3001 4.9 28.5 1.0
CA B:ASP330 5.0 15.2 1.0

Manganese binding site 4 out of 8 in 2fah

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Manganese binding site 4 out of 8 in the The Structure of Mitochondrial Pepck, Complex with Mn and Gdp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of The Structure of Mitochondrial Pepck, Complex with Mn and Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn3003

b:23.1
occ:0.30
 O2A B:GDP3000 2.5 17.2 1.0
N B:VAL354 2.7 14.5 1.0
O1B B:GDP3000 3.1 16.1 1.0
CA B:GLY353 3.2 14.8 1.0
O2B B:GDP3000 3.2 17.2 1.0
OG1 B:THR310 3.3 15.6 1.0
O B:HOH6068 3.4 15.3 1.0
C B:GLY353 3.4 14.9 1.0
CG2 B:VAL354 3.5 14.5 1.0
PB B:GDP3000 3.5 15.7 1.0
CB B:VAL354 3.6 14.9 1.0
PA B:GDP3000 3.7 15.8 1.0
CA B:VAL354 3.7 14.8 1.0
NH1 B:ARG424 3.7 15.9 1.0
O3A B:GDP3000 3.8 18.9 1.0
O B:HOH6037 3.9 16.9 1.0
CB B:THR310 4.0 15.1 1.0
O B:PHE352 4.1 15.0 1.0
O B:HOH6100 4.1 20.8 1.0
N B:GLY353 4.4 14.9 1.0
CZ B:ARG424 4.6 17.1 1.0
O1A B:GDP3000 4.6 16.9 1.0
O B:VAL354 4.6 14.7 1.0
O B:GLY353 4.6 15.1 1.0
C B:VAL354 4.7 15.0 1.0
C B:PHE352 4.7 15.2 1.0
O5' B:GDP3000 4.8 16.7 1.0
CG2 B:THR310 4.8 15.0 1.0
C5' B:GDP3000 5.0 17.7 1.0
O3B B:GDP3000 5.0 15.9 1.0

Manganese binding site 5 out of 8 in 2fah

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Manganese binding site 5 out of 8 in the The Structure of Mitochondrial Pepck, Complex with Mn and Gdp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of The Structure of Mitochondrial Pepck, Complex with Mn and Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn4001

b:9.9
occ:0.90
 NZ C:LYS263 2.0 16.1 1.0
O1A C:MLA4003 2.0 24.8 1.0
OD1 C:ASP330 2.1 16.3 1.0
NE2 C:HIS283 2.2 14.7 1.0
O C:HOH6005 2.3 12.0 1.0
O3A C:MLA4003 2.5 21.0 1.0
C1 C:MLA4003 2.8 26.3 1.0
CG C:ASP330 3.0 15.4 1.0
CD2 C:HIS283 3.1 14.8 1.0
CE C:LYS263 3.1 15.3 1.0
OD2 C:ASP330 3.2 15.5 1.0
CE1 C:HIS283 3.2 15.4 1.0
O1B C:MLA4003 3.4 30.4 1.0
C3 C:MLA4003 3.4 21.8 1.0
C2 C:MLA4003 3.6 22.5 1.0
NZ C:LYS309 3.8 10.8 0.5
CE C:LYS309 3.9 10.0 0.5
OG C:SER305 4.1 17.4 1.0
O C:HOH6273 4.1 22.5 1.0
NZ C:LYS309 4.2 3.4 0.5
CG C:HIS283 4.3 15.1 1.0
ND1 C:HIS283 4.3 15.6 1.0
O C:HOH6207 4.3 20.5 1.0
CD C:LYS263 4.4 14.8 1.0
CB C:ASP330 4.4 15.0 1.0
O C:HOH6282 4.5 10.7 1.0
O3B C:MLA4003 4.6 21.9 1.0
CB C:SER305 4.8 15.5 1.0
CZ C:PHE504 4.8 13.7 1.0
CA C:SER305 4.8 15.9 1.0
CE C:LYS309 4.8 11.4 0.5
CE2 C:PHE504 4.9 14.6 1.0
CA C:ASP330 4.9 15.2 1.0
O C:ASP330 4.9 15.3 1.0

Manganese binding site 6 out of 8 in 2fah

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Manganese binding site 6 out of 8 in the The Structure of Mitochondrial Pepck, Complex with Mn and Gdp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of The Structure of Mitochondrial Pepck, Complex with Mn and Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn4002

b:9.5
occ:0.30
 O C:HOH6321 2.3 28.5 1.0
O2A C:GDP4000 2.6 11.0 1.0
O1B C:GDP4000 2.7 11.4 1.0
O2B C:GDP4000 2.7 12.8 1.0
PB C:GDP4000 3.2 14.3 1.0
N C:VAL354 3.2 14.7 1.0
OG1 C:THR310 3.2 15.3 1.0
PA C:GDP4000 3.6 13.1 1.0
CG2 C:VAL354 3.6 14.5 1.0
CA C:GLY353 3.7 14.8 1.0
O3A C:GDP4000 3.7 12.2 1.0
O C:HOH6124 3.8 11.3 1.0
O C:HOH6282 3.9 10.7 1.0
CB C:VAL354 3.9 14.9 1.0
C C:GLY353 3.9 14.8 1.0
NH1 C:ARG424 4.0 15.9 1.0
CB C:THR310 4.1 15.2 1.0
CA C:VAL354 4.1 14.7 1.0
O C:HOH6273 4.2 22.5 1.0
O1B C:MLA4003 4.2 30.4 1.0
O C:PHE352 4.3 15.2 1.0
O1A C:GDP4000 4.5 13.5 1.0
O3B C:GDP4000 4.6 13.2 1.0
O C:HOH6005 4.8 12.0 1.0
CZ C:ARG424 4.8 16.9 1.0
O5' C:GDP4000 4.8 13.4 1.0
N C:GLY353 4.8 15.2 1.0
C C:PHE352 5.0 15.1 1.0
CG2 C:THR310 5.0 14.8 1.0
N C:THR310 5.0 15.5 1.0

Manganese binding site 7 out of 8 in 2fah

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Manganese binding site 7 out of 8 in the The Structure of Mitochondrial Pepck, Complex with Mn and Gdp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of The Structure of Mitochondrial Pepck, Complex with Mn and Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn5002

b:38.9
occ:0.50
 O D:HOH6202 1.9 22.3 1.0
NZ D:LYS263 2.0 16.7 1.0
NE2 D:HIS283 2.1 14.8 1.0
OD1 D:ASP330 2.3 16.4 1.0
O3A D:MLA5001 2.6 32.4 1.0
CE1 D:HIS283 3.1 15.2 1.0
CD2 D:HIS283 3.1 15.0 1.0
CE D:LYS263 3.2 15.1 1.0
CG D:ASP330 3.3 15.5 1.0
OG D:SER305 3.5 17.6 1.0
OD2 D:ASP330 3.6 16.3 1.0
C3 D:MLA5001 3.7 32.1 1.0
NZ D:LYS309 3.9 11.0 1.0
O D:HOH6201 4.0 31.0 1.0
CE D:LYS309 4.1 13.1 1.0
ND1 D:HIS283 4.2 15.5 1.0
O D:HOH6134 4.3 24.5 1.0
CG D:HIS283 4.3 15.2 1.0
CB D:SER305 4.3 15.6 1.0
O3B D:MLA5001 4.4 31.8 1.0
CD D:LYS263 4.4 14.8 1.0
CA D:SER305 4.4 15.7 1.0
CB D:ASP330 4.7 15.0 1.0
CZ D:PHE504 4.7 14.0 1.0
C2 D:MLA5001 4.8 30.7 1.0
CE2 D:PHE504 4.8 14.7 1.0
N D:SER305 4.9 15.8 1.0

Manganese binding site 8 out of 8 in 2fah

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Manganese binding site 8 out of 8 in the The Structure of Mitochondrial Pepck, Complex with Mn and Gdp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of The Structure of Mitochondrial Pepck, Complex with Mn and Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn5003

b:14.9
occ:0.30
 O1A D:GDP5000 2.6 16.9 1.0
O2B D:GDP5000 2.8 22.1 1.0
N D:VAL354 2.9 14.7 1.0
OG1 D:THR310 3.1 15.3 1.0
O1B D:GDP5000 3.2 24.7 1.0
CA D:GLY353 3.2 14.9 1.0
PB D:GDP5000 3.4 23.9 1.0
C D:GLY353 3.5 14.9 1.0
O D:HOH6236 3.7 28.7 1.0
CG2 D:VAL354 3.7 14.3 1.0
O D:HOH6033 3.8 17.6 1.0
PA D:GDP5000 3.8 19.6 1.0
NH1 D:ARG424 3.9 15.2 1.0
CB D:VAL354 3.9 15.0 1.0
CB D:THR310 3.9 15.1 1.0
O3A D:GDP5000 3.9 21.6 1.0
CA D:VAL354 4.0 14.8 1.0
O D:PHE352 4.0 15.3 1.0
O D:HOH6201 4.1 31.0 1.0
N D:GLY353 4.4 15.0 1.0
C D:PHE352 4.6 15.2 1.0
O2A D:GDP5000 4.7 18.3 1.0
CG2 D:THR310 4.7 14.8 1.0
O D:GLY353 4.8 15.1 1.0
OD2 D:ASP329 4.8 19.0 1.0
CZ D:ARG424 4.8 15.8 1.0
O3B D:GDP5000 4.8 24.6 1.0
O D:VAL354 4.8 14.9 1.0
C D:VAL354 4.9 15.1 1.0

Reference:

T.Holyoak, S.M.Sullivan, T.Nowak. Structural Insights Into the Mechanism of Pepck Catalysis Biochemistry V. 45 8254 2006.
ISSN: ISSN 0006-2960
PubMed: 16819824
DOI: 10.1021/BI060269G
Page generated: Sat Oct 5 14:03:26 2024

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