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Magnesium in PDB 3b6b: Crystal Structure of Acanthamoeba Polyphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Dgdp

Enzymatic activity of Crystal Structure of Acanthamoeba Polyphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Dgdp

All present enzymatic activity of Crystal Structure of Acanthamoeba Polyphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Dgdp:
2.7.4.6;

Protein crystallography data

The structure of Crystal Structure of Acanthamoeba Polyphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Dgdp, PDB code: 3b6b was solved by S.Jeudy, A.Lartigue, J.M.Claverie, C.Abergel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.00
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 79.839, 152.528, 184.120, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 22.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Acanthamoeba Polyphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Dgdp (pdb code 3b6b). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of Acanthamoeba Polyphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Dgdp, PDB code: 3b6b:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3b6b

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Magnesium binding site 1 out of 6 in the Crystal Structure of Acanthamoeba Polyphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Dgdp


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 Acanthamoeba Polyphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Dgdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg138

b:40.6
occ:1.00
 O3A A:DGI139 2.4 71.4 1.0
O5' A:DGI139 3.0 68.7 1.0
NH1 A:ARG99 3.4 26.9 1.0
PA A:DGI139 3.5 70.2 1.0
O A:HOH181 3.5 39.4 1.0
O3' A:DGI139 3.5 61.4 1.0
PB A:DGI139 3.5 72.4 1.0
NH2 A:ARG99 3.5 25.7 1.0
O1A A:DGI139 3.6 70.3 1.0
C5' A:DGI139 3.7 66.1 1.0
NH2 A:ARG86 3.7 42.3 1.0
O2B A:DGI139 3.7 71.3 1.0
CZ A:ARG99 3.9 26.4 1.0
C3' A:DGI139 3.9 63.5 1.0
O1B A:DGI139 4.0 71.3 1.0
C4' A:DGI139 4.4 64.6 1.0
CZ A:ARG86 4.6 41.7 1.0
O2A A:DGI139 4.7 71.6 1.0
NE2 A:GLN89 4.7 34.1 1.0
NH1 A:ARG86 4.8 42.0 1.0
O3B A:DGI139 4.9 71.4 1.0
ND2 A:ASN109 4.9 28.5 1.0

Magnesium binding site 2 out of 6 in 3b6b

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Magnesium binding site 2 out of 6 in the Crystal Structure of Acanthamoeba Polyphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Dgdp


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 Acanthamoeba Polyphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Dgdp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg138

b:80.3
occ:1.00
 O3B B:DGI140 1.8 61.8 1.0
O3' B:DGI140 2.1 58.6 1.0
PB B:DGI140 3.1 61.7 1.0
O1B B:DGI140 3.4 61.8 1.0
C3' B:DGI140 3.4 57.1 1.0
CE1 B:HIS53 3.5 45.7 1.0
O2B B:DGI140 3.9 59.2 1.0
NE2 B:HIS53 4.0 45.9 1.0
C4' B:DGI140 4.2 56.9 1.0
O5' B:DGI140 4.3 58.3 1.0
O3A B:DGI140 4.4 60.0 1.0
C2' B:DGI140 4.5 56.2 1.0
ND1 B:HIS53 4.7 45.9 1.0
C5' B:DGI140 4.8 57.1 1.0
PA B:DGI140 4.9 57.0 1.0

Magnesium binding site 3 out of 6 in 3b6b

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Magnesium binding site 3 out of 6 in the Crystal Structure of Acanthamoeba Polyphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Dgdp


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 Acanthamoeba Polyphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Dgdp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg138

b:58.4
occ:1.00
 O2B C:DGI141 2.1 57.3 1.0
O2A C:DGI141 2.3 56.5 1.0
O C:HOH185 3.2 47.7 1.0
PB C:DGI141 3.3 57.8 1.0
PA C:DGI141 3.5 54.8 1.0
O3A C:DGI141 3.7 56.7 1.0
O1B C:DGI141 3.7 59.3 1.0
O3' C:DGI141 3.9 56.3 1.0
O1A C:DGI141 4.1 52.9 1.0
NH2 C:ARG86 4.1 43.6 1.0
NE2 C:HIS53 4.1 40.6 1.0
ND1 C:HIS112 4.3 30.8 1.0
CE1 C:HIS112 4.3 30.4 1.0
CE1 C:HIS53 4.5 40.5 1.0
O3B C:DGI141 4.6 57.8 1.0
C3' C:DGI141 4.7 55.6 1.0
O5' C:DGI141 4.8 56.9 1.0
O C:HOH195 4.9 34.1 1.0
CE2 C:TYR50 5.0 34.2 1.0

Magnesium binding site 4 out of 6 in 3b6b

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Magnesium binding site 4 out of 6 in the Crystal Structure of Acanthamoeba Polyphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Dgdp


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 Acanthamoeba Polyphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Dgdp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg138

b:42.6
occ:1.00
 O2B D:DGI142 1.7 63.1 1.0
O2A D:DGI142 1.9 60.7 1.0
PB D:DGI142 3.0 64.7 1.0
PA D:DGI142 3.1 59.2 1.0
O3A D:DGI142 3.3 61.5 1.0
NH2 D:ARG86 3.5 46.6 1.0
NH1 D:ARG99 3.6 27.0 1.0
O3' D:DGI142 3.6 56.0 1.0
NH2 D:ARG99 3.7 26.2 1.0
O D:HOH186 3.7 37.7 1.0
C5' D:DGI142 3.8 57.5 1.0
O5' D:DGI142 3.9 59.1 1.0
O1B D:DGI142 3.9 63.3 1.0
O3B D:DGI142 4.1 62.7 1.0
CZ D:ARG99 4.1 27.1 1.0
C3' D:DGI142 4.1 55.9 1.0
O1A D:DGI142 4.2 59.7 1.0
C4' D:DGI142 4.5 56.9 1.0
CZ D:ARG86 4.7 45.5 1.0
OE1 D:GLN89 4.9 36.5 1.0

Magnesium binding site 5 out of 6 in 3b6b

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Magnesium binding site 5 out of 6 in the Crystal Structure of Acanthamoeba Polyphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Dgdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Acanthamoeba Polyphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Dgdp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg138

b:51.7
occ:1.00
 O1A E:DGI143 2.6 65.6 1.0
O1B E:DGI143 2.6 64.4 1.0
PB E:DGI143 3.3 63.9 1.0
O2B E:DGI143 3.3 63.7 1.0
C5' E:DGI143 3.5 66.3 1.0
PA E:DGI143 3.5 66.4 1.0
O3A E:DGI143 3.7 65.5 1.0
O E:HOH202 3.9 42.5 1.0
O5' E:DGI143 4.0 66.0 1.0
NE2 E:HIS53 4.1 49.9 1.0
NH2 E:ARG86 4.1 38.0 1.0
ND1 E:HIS112 4.3 28.8 1.0
CE1 E:HIS53 4.3 49.7 1.0
CE1 E:HIS112 4.3 29.2 1.0
C4' E:DGI143 4.7 66.5 1.0
O E:HOH210 4.8 32.3 1.0
CE2 E:TYR50 4.8 41.0 1.0
O3B E:DGI143 4.8 63.5 1.0
O3' E:DGI143 4.9 66.0 1.0

Magnesium binding site 6 out of 6 in 3b6b

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Magnesium binding site 6 out of 6 in the Crystal Structure of Acanthamoeba Polyphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Dgdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Acanthamoeba Polyphaga Mimivirus Nucleoside Diphosphate Kinase Complexed with Dgdp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg138

b:51.1
occ:1.00
 O1B F:DGI144 2.3 65.7 1.0
O3' F:DGI144 2.3 66.0 1.0
O2B F:DGI144 2.7 65.6 1.0
PB F:DGI144 3.0 65.0 1.0
O2A F:DGI144 3.2 66.4 1.0
C3' F:DGI144 3.5 66.6 1.0
C4' F:DGI144 3.7 66.5 1.0
CE1 F:HIS53 3.9 53.6 1.0
O3A F:DGI144 4.1 65.5 1.0
PA F:DGI144 4.2 66.0 1.0
O3B F:DGI144 4.2 65.2 1.0
NE2 F:HIS53 4.4 53.7 1.0
O5' F:DGI144 4.4 65.5 1.0
C2' F:DGI144 4.5 66.9 1.0
C5' F:DGI144 4.6 65.8 1.0
O4' F:DGI144 4.7 67.4 1.0
C1' F:DGI144 4.8 67.0 1.0
ND1 F:HIS53 5.0 53.4 1.0

Reference:

S.Jeudy, A.Lartigue, J.M.Claverie, C.Abergel. Dissecting the Unique Nucleotide Specificity of Mimivirus Nucleoside Diphosphate Kinase. J.Virol. V. 83 7142 2009.
ISSN: ISSN 0022-538X
PubMed: 19439473
DOI: 10.1128/JVI.00511-09
Page generated: Wed Aug 14 08:51:59 2024

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