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Magnesium in PDB 5yih: Crystal Structure of Tetrameric Nucleoside Diphosphate Kinase at 1.98 A Resolution From Acinetobacter Baumannii

Enzymatic activity of Crystal Structure of Tetrameric Nucleoside Diphosphate Kinase at 1.98 A Resolution From Acinetobacter Baumannii

All present enzymatic activity of Crystal Structure of Tetrameric Nucleoside Diphosphate Kinase at 1.98 A Resolution From Acinetobacter Baumannii:
2.7.4.6;

Protein crystallography data

The structure of Crystal Structure of Tetrameric Nucleoside Diphosphate Kinase at 1.98 A Resolution From Acinetobacter Baumannii, PDB code: 5yih was solved by H.R.Bairagya, J.Sikarwar, N.Iqbal, P.K.Singh, P.Kaur, S.Sharma, T.P.Singh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 68.80 / 1.98
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 145.880, 70.470, 68.850, 90.00, 109.40, 90.00
R / Rfree (%) 20.2 / 25.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Tetrameric Nucleoside Diphosphate Kinase at 1.98 A Resolution From Acinetobacter Baumannii (pdb code 5yih). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of Tetrameric Nucleoside Diphosphate Kinase at 1.98 A Resolution From Acinetobacter Baumannii, PDB code: 5yih:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 5yih

Go back to Magnesium Binding Sites List in 5yih
Magnesium binding site 1 out of 5 in the Crystal Structure of Tetrameric Nucleoside Diphosphate Kinase at 1.98 A Resolution From Acinetobacter Baumannii


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 Tetrameric Nucleoside Diphosphate Kinase at 1.98 A Resolution From Acinetobacter Baumannii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg201

b:18.5
occ:1.00
 O A:HOH335 2.0 31.4 1.0
OD2 A:ASP112 2.2 41.6 1.0
OD1 A:ASP112 2.8 47.3 1.0
CG A:ASP112 2.9 45.9 1.0
OD2 A:ASP62 4.1 30.1 1.0
O A:HOH342 4.4 33.5 1.0
CB A:ASP112 4.4 39.0 1.0

Magnesium binding site 2 out of 5 in 5yih

Go back to Magnesium Binding Sites List in 5yih
Magnesium binding site 2 out of 5 in the Crystal Structure of Tetrameric Nucleoside Diphosphate Kinase at 1.98 A Resolution From Acinetobacter Baumannii


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 Tetrameric Nucleoside Diphosphate Kinase at 1.98 A Resolution From Acinetobacter Baumannii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:33.2
occ:1.00
 O A:HOH307 1.9 46.7 1.0
O C:HOH309 2.1 38.7 1.0
OD1 A:ASN136 2.2 41.0 1.0
O A:ASN136 2.3 38.9 1.0
O A:HOH324 2.4 51.8 1.0
OD1 C:ASP46 2.6 42.6 1.0
CG A:ASN136 3.2 40.0 1.0
C A:ASN136 3.4 38.7 1.0
CG C:ASP46 3.7 42.4 1.0
CA A:ASN136 3.8 39.1 1.0
O D:HOH367 4.0 48.4 1.0
O C:HOH376 4.1 54.4 1.0
CB A:ASN136 4.1 37.8 1.0
ND2 A:ASN136 4.1 41.2 1.0
O D:HOH313 4.4 47.9 1.0
N A:GLU137 4.5 38.0 1.0
OD2 C:ASP46 4.5 43.6 1.0
CA C:ASP46 4.6 36.3 1.0
CB C:ASP46 4.6 36.1 1.0
O A:ILE138 4.9 46.4 1.0
OH C:TYR131 4.9 32.4 1.0
CA A:GLU137 5.0 35.4 1.0
N C:ASP46 5.0 32.7 1.0

Magnesium binding site 3 out of 5 in 5yih

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Magnesium binding site 3 out of 5 in the Crystal Structure of Tetrameric Nucleoside Diphosphate Kinase at 1.98 A Resolution From Acinetobacter Baumannii


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 Tetrameric Nucleoside Diphosphate Kinase at 1.98 A Resolution From Acinetobacter Baumannii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg203

b:29.4
occ:1.00
 O C:HOH312 2.3 35.7 1.0
O C:HOH339 2.3 43.0 1.0
OD1 A:ASP46 2.4 39.3 1.0
O A:HOH351 2.5 54.6 1.0
OD1 C:ASN136 2.5 37.7 1.0
O C:ASN136 2.6 41.5 1.0
O C:HOH354 2.9 40.7 1.0
CG C:ASN136 3.4 38.8 1.0
O C:HOH304 3.5 51.9 1.0
CG A:ASP46 3.5 33.9 1.0
C C:ASN136 3.6 35.2 1.0
CA C:ASN136 4.0 35.6 1.0
ND2 C:ASN136 4.3 37.3 1.0
CB C:ASN136 4.3 35.3 1.0
OD2 A:ASP46 4.3 36.9 1.0
CA A:ASP46 4.4 27.8 1.0
CB A:ASP46 4.4 29.9 1.0
O B:HOH262 4.5 39.7 1.0
O A:HOH316 4.5 42.0 1.0
N A:ASP46 4.7 24.6 1.0
N C:GLU137 4.8 36.7 1.0
OH A:TYR131 4.9 31.4 1.0

Magnesium binding site 4 out of 5 in 5yih

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Magnesium binding site 4 out of 5 in the Crystal Structure of Tetrameric Nucleoside Diphosphate Kinase at 1.98 A Resolution From Acinetobacter Baumannii


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 Tetrameric Nucleoside Diphosphate Kinase at 1.98 A Resolution From Acinetobacter Baumannii within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg201

b:40.9
occ:1.00
 O C:HOH333 2.2 51.3 1.0
O C:HOH328 2.3 46.4 1.0
OD2 C:ASP112 2.3 61.0 1.0
CG C:ASP112 3.4 59.3 1.0
OD1 C:ASP112 3.7 57.2 1.0
OD2 C:ASP62 3.9 45.6 1.0
CB C:ASP112 4.7 53.3 1.0
CG C:ASP62 4.8 47.1 1.0
CB C:ASP62 4.8 40.7 1.0

Magnesium binding site 5 out of 5 in 5yih

Go back to Magnesium Binding Sites List in 5yih
Magnesium binding site 5 out of 5 in the Crystal Structure of Tetrameric Nucleoside Diphosphate Kinase at 1.98 A Resolution From Acinetobacter Baumannii


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 Tetrameric Nucleoside Diphosphate Kinase at 1.98 A Resolution From Acinetobacter Baumannii within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg201

b:48.2
occ:1.00
 O D:HOH335 1.9 53.4 1.0
O D:HOH301 2.1 41.9 1.0
O B:HOH238 2.3 44.9 1.0
O B:HOH298 2.3 47.1 1.0
OD1 D:ASN136 2.6 43.3 1.0
O B:HOH216 2.6 39.2 1.0
O D:ASN136 3.0 28.9 1.0
CA D:ASN136 3.6 33.3 1.0
CG D:ASN136 3.6 41.0 1.0
C D:ASN136 3.7 33.0 1.0
OH B:TYR131 3.9 27.2 1.0
OD1 B:ASP46 4.0 32.1 1.0
CB D:ASN136 4.1 33.2 1.0
O D:HOH338 4.5 46.6 1.0
CZ B:TYR131 4.6 29.0 1.0
O D:ILE138 4.7 31.4 1.0
ND2 D:ASN136 4.7 47.0 1.0
CA B:ASP46 4.8 28.2 1.0
N D:ASN136 4.8 35.2 1.0
O D:ASP135 4.8 28.8 1.0
O B:ALA45 4.9 29.0 1.0
CE1 B:TYR131 4.9 28.4 1.0
N D:GLU137 5.0 29.9 1.0

Reference:

H.R.Bairagya, J.Sikarwar, N.Iqbal, P.K.Singh, P.Kaur, S.Sharma, T.P.Singh. Crystal Structure of Tetrameric Nucleoside Diphosphate Kinase at 1.98 A Resolution From Acinetobacter Baumannii To Be Published.
Page generated: Wed Aug 13 00:56:04 2025

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