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Magnesium in PDB 2vpq: Crystal Structure of Biotin Carboxylase From S. Aureus Complexed with Amppnp

Enzymatic activity of Crystal Structure of Biotin Carboxylase From S. Aureus Complexed with Amppnp

All present enzymatic activity of Crystal Structure of Biotin Carboxylase From S. Aureus Complexed with Amppnp:
6.3.4.14;

Protein crystallography data

The structure of Crystal Structure of Biotin Carboxylase From S. Aureus Complexed with Amppnp, PDB code: 2vpq was solved by I.Mochalkin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.1
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 78.247, 63.318, 105.142, 90.00, 103.82, 90.00
R / Rfree (%) 21.5 / 28.4

Other elements in 2vpq:

The structure of Crystal Structure of Biotin Carboxylase From S. Aureus Complexed with Amppnp also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Biotin Carboxylase From S. Aureus Complexed with Amppnp (pdb code 2vpq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Biotin Carboxylase From S. Aureus Complexed with Amppnp, PDB code: 2vpq:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2vpq

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Magnesium binding site 1 out of 4 in the Crystal Structure of Biotin Carboxylase From S. Aureus Complexed with Amppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Biotin Carboxylase From S. Aureus Complexed with Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1450

b:16.7
occ:1.00
 O1G A:ANP1449 1.9 24.0 1.0
OE1 A:GLU274 2.0 21.2 1.0
O2A A:ANP1449 2.1 18.8 1.0
O A:HOH2417 2.2 24.4 1.0
OE1 A:GLU288 2.4 19.8 1.0
OE2 A:GLU274 2.5 20.2 1.0
CD A:GLU274 2.6 20.2 1.0
PG A:ANP1449 3.1 25.6 1.0
CD A:GLU288 3.4 21.5 1.0
N3B A:ANP1449 3.5 22.0 1.0
O2G A:ANP1449 3.6 25.0 1.0
PA A:ANP1449 3.6 17.5 1.0
CG A:GLU288 3.8 21.4 1.0
ND2 A:ASN290 3.8 25.3 1.0
CG A:GLU274 4.0 19.6 1.0
MG A:MG1451 4.1 18.8 1.0
O1B A:ANP1449 4.2 21.0 1.0
PB A:ANP1449 4.2 20.5 1.0
CE A:MET287 4.2 19.2 1.0
O3A A:ANP1449 4.3 18.8 1.0
O3G A:ANP1449 4.4 23.2 1.0
OE2 A:GLU288 4.4 19.5 1.0
O5' A:ANP1449 4.5 20.6 1.0
OD1 A:ASN290 4.5 30.2 1.0
O1A A:ANP1449 4.6 15.4 1.0
CG A:ASN290 4.6 26.0 1.0
C5' A:ANP1449 4.7 21.5 1.0
O3' A:ANP1449 4.7 21.9 1.0
CB A:GLU274 4.7 19.5 1.0
CE1 A:HIS207 4.8 24.3 1.0
O A:HOH2266 5.0 36.3 1.0

Magnesium binding site 2 out of 4 in 2vpq

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Magnesium binding site 2 out of 4 in the Crystal Structure of Biotin Carboxylase From S. Aureus Complexed with Amppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Biotin Carboxylase From S. Aureus Complexed with Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1451

b:18.8
occ:1.00
 O2G A:ANP1449 1.8 25.0 1.0
O A:HOH2266 1.9 36.3 1.0
O A:HOH2172 2.0 21.6 1.0
O1B A:ANP1449 2.1 21.0 1.0
OE1 A:GLU288 2.2 19.8 1.0
OE2 A:GLU288 2.3 19.5 1.0
CD A:GLU288 2.6 21.5 1.0
PG A:ANP1449 3.1 25.6 1.0
PB A:ANP1449 3.3 20.5 1.0
ND2 A:ASN290 3.4 25.3 1.0
N3B A:ANP1449 3.6 22.0 1.0
O1G A:ANP1449 3.8 24.0 1.0
O A:HOH2264 3.9 18.1 1.0
O A:GLY161 4.0 25.7 1.0
MG A:MG1450 4.1 16.7 1.0
CG A:GLU288 4.1 21.4 1.0
NZ A:LYS115 4.2 21.8 1.0
OE2 A:GLU86 4.2 27.6 1.0
O3G A:ANP1449 4.2 23.2 1.0
O3A A:ANP1449 4.4 18.8 1.0
O2A A:ANP1449 4.4 18.8 1.0
O2B A:ANP1449 4.4 19.4 1.0
CA A:GLY162 4.5 26.4 1.0
CG A:ASN290 4.7 26.0 1.0
CE A:LYS115 4.8 23.9 1.0
O A:MET289 4.8 22.9 1.0
PA A:ANP1449 4.8 17.5 1.0
O A:HOH2173 4.9 36.5 1.0
CD A:LYS115 4.9 23.2 1.0
C A:GLY161 4.9 26.0 1.0
CB A:GLU288 5.0 21.9 1.0
OE1 A:GLU86 5.0 26.2 1.0

Magnesium binding site 3 out of 4 in 2vpq

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Magnesium binding site 3 out of 4 in the Crystal Structure of Biotin Carboxylase From S. Aureus Complexed with Amppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Biotin Carboxylase From S. Aureus Complexed with Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1451

b:29.5
occ:1.00
 O3G B:ANP1450 1.9 21.7 1.0
O2A B:ANP1450 1.9 23.5 1.0
OE1 B:GLU274 2.0 24.7 1.0
O B:HOH2398 2.0 18.3 1.0
OE1 B:GLU288 2.6 25.6 1.0
CD B:GLU274 2.8 23.6 1.0
OE2 B:GLU274 2.8 26.4 1.0
PG B:ANP1450 3.1 23.1 1.0
N3B B:ANP1450 3.4 23.1 1.0
PA B:ANP1450 3.4 22.6 1.0
CD B:GLU288 3.5 24.0 1.0
O1G B:ANP1450 3.9 24.6 1.0
CG B:GLU288 3.9 24.2 1.0
PB B:ANP1450 4.1 23.9 1.0
O3A B:ANP1450 4.1 23.4 1.0
CG B:GLU274 4.2 22.1 1.0
O1B B:ANP1450 4.2 24.9 1.0
ND2 B:ASN290 4.3 24.1 1.0
O2G B:ANP1450 4.3 25.6 1.0
MG B:MG1452 4.3 27.5 1.0
O5' B:ANP1450 4.3 23.5 1.0
O3' B:ANP1450 4.3 21.9 1.0
O1A B:ANP1450 4.4 22.2 1.0
OD1 B:ASN290 4.4 28.0 1.0
C5' B:ANP1450 4.4 23.9 1.0
CE B:MET287 4.5 24.9 1.0
OE2 B:GLU288 4.5 24.8 1.0
O B:HOH2209 4.6 27.8 1.0
CE1 B:HIS207 4.7 26.1 1.0
CG B:ASN290 4.8 25.0 1.0
CB B:GLU274 4.8 22.0 1.0
C3' B:ANP1450 4.8 23.2 1.0
O B:HOH2396 5.0 24.3 1.0
NZ B:LYS236 5.0 28.6 1.0

Magnesium binding site 4 out of 4 in 2vpq

Go back to Magnesium Binding Sites List in 2vpq
Magnesium binding site 4 out of 4 in the Crystal Structure of Biotin Carboxylase From S. Aureus Complexed with Amppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Biotin Carboxylase From S. Aureus Complexed with Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1452

b:27.5
occ:1.00
 O1G B:ANP1450 1.8 24.6 1.0
O B:HOH2243 1.8 19.9 1.0
O1B B:ANP1450 1.9 24.9 1.0
O B:HOH2155 2.1 13.2 1.0
OE1 B:GLU288 2.4 25.6 1.0
OE2 B:GLU288 2.4 24.8 1.0
CD B:GLU288 2.7 24.0 1.0
PG B:ANP1450 3.0 23.1 1.0
PB B:ANP1450 3.2 23.9 1.0
ND2 B:ASN290 3.2 24.1 1.0
N3B B:ANP1450 3.5 23.1 1.0
O B:HOH2393 3.7 34.9 1.0
O3G B:ANP1450 3.7 21.7 1.0
O2B B:ANP1450 4.2 23.4 1.0
O2G B:ANP1450 4.2 25.6 1.0
CG B:GLU288 4.2 24.2 1.0
O B:HOH2242 4.2 16.1 1.0
O B:GLY161 4.3 27.3 1.0
O3A B:ANP1450 4.3 23.4 1.0
MG B:MG1451 4.3 29.5 1.0
CA B:GLY162 4.4 28.6 1.0
NZ B:LYS115 4.4 23.6 1.0
O2A B:ANP1450 4.4 23.5 1.0
CG B:ASN290 4.5 25.0 1.0
OE2 B:GLU86 4.7 29.1 1.0
OE1 B:GLU86 4.7 27.8 1.0
CE B:LYS115 4.8 25.1 1.0
O B:MET289 4.8 23.6 1.0
PA B:ANP1450 4.8 22.6 1.0

Reference:

I.Mochalkin, J.R.Miller, A.Evdokimov, S.Lightle, C.Yan, C.K.Stover, G.L.Waldrop. Structural Evidence For Substrate-Induced Synergism and Half-Sites Reactivity in Biotin Carboxylase. Protein Sci. V. 17 1706 2008.
ISSN: ISSN 0961-8368
PubMed: 18725455
DOI: 10.1110/PS.035584.108
Page generated: Wed Aug 14 05:18:01 2024

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