Atomistry » Magnesium » PDB 5y4n-5ylu » 5yih
Atomistry »
  Magnesium »
    PDB 5y4n-5ylu »
      5yih »

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

Go back to Magnesium Binding Sites List in 5yih
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

Go back to Magnesium Binding Sites List in 5yih
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: Mon Sep 30 11:10:13 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy