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Magnesium in PDB 2nv1: Structure of the Synthase Subunit PDX1 (Yaad) of Plp Synthase From Bacillus Subtilis

Protein crystallography data

The structure of Structure of the Synthase Subunit PDX1 (Yaad) of Plp Synthase From Bacillus Subtilis, PDB code: 2nv1 was solved by M.Strohmeier, I.Tews, I.Sinning, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.68 / 2.08
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 101.055, 106.202, 182.332, 90.00, 90.00, 90.00
R / Rfree (%) 14.2 / 19.1

Other elements in 2nv1:

The structure of Structure of the Synthase Subunit PDX1 (Yaad) of Plp Synthase From Bacillus Subtilis also contains other interesting chemical elements:

Chlorine (Cl) 12 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the Structure of the Synthase Subunit PDX1 (Yaad) of Plp Synthase From Bacillus Subtilis (pdb code 2nv1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Structure of the Synthase Subunit PDX1 (Yaad) of Plp Synthase From Bacillus Subtilis, PDB code: 2nv1:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in 2nv1

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Magnesium binding site 1 out of 12 in the Structure of the Synthase Subunit PDX1 (Yaad) of Plp Synthase From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Synthase Subunit PDX1 (Yaad) of Plp Synthase From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3003

b:61.8
occ:1.00
 O A:HOH4003 2.2 58.9 1.0
O F:HOH4005 2.2 57.9 1.0
O F:HOH4004 2.2 57.7 1.0
O A:HOH4001 2.2 60.0 1.0
O A:HOH4002 2.2 60.4 1.0
O A:HOH4004 2.2 60.7 1.0
OE2 A:GLU112 4.1 40.2 1.0
OE1 A:GLU112 4.2 40.7 1.0
OE2 F:GLU159 4.2 43.5 1.0
O F:HOH4170 4.3 56.4 1.0
OE2 F:GLU151 4.4 49.2 1.0
CD A:GLU112 4.6 38.7 1.0
O F:HOH4307 4.7 73.5 1.0
CG1 F:VAL158 4.8 30.5 1.0
O F:HOH4159 5.0 55.2 1.0
O F:HOH4327 5.0 76.2 1.0

Magnesium binding site 2 out of 12 in 2nv1

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Magnesium binding site 2 out of 12 in the Structure of the Synthase Subunit PDX1 (Yaad) of Plp Synthase From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Synthase Subunit PDX1 (Yaad) of Plp Synthase From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3004

b:67.8
occ:1.00
 O A:HOH4005 2.2 68.0 1.0
O A:HOH4010 2.2 66.5 1.0
O A:HOH4006 2.2 67.4 1.0
O A:HOH4008 2.2 69.3 1.0
O A:HOH4009 2.2 67.9 1.0
O A:HOH4007 2.2 69.1 1.0
O A:HOH4108 4.1 47.4 1.0
O A:VAL74 4.2 38.8 1.0
O A:MET71 4.2 37.9 1.0
OD2 A:ASP99 4.4 32.8 1.0
O A:HOH4293 4.4 74.1 1.0
O A:ILE76 4.4 35.6 1.0
O A:HOH4270 4.4 70.9 1.0
O A:HOH4305 4.7 75.3 1.0
O A:SER75 4.7 43.5 1.0
O A:HOH4295 4.8 74.2 1.0
C A:SER75 4.8 41.0 1.0
CA A:SER75 4.9 41.6 1.0

Magnesium binding site 3 out of 12 in 2nv1

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Magnesium binding site 3 out of 12 in the Structure of the Synthase Subunit PDX1 (Yaad) of Plp Synthase From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the Synthase Subunit PDX1 (Yaad) of Plp Synthase From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3009

b:61.9
occ:1.00
 O B:HOH4016 2.2 56.3 1.0
O B:HOH4015 2.2 56.6 1.0
O A:HOH4011 2.2 60.5 1.0
O A:HOH4013 2.2 56.6 1.0
O B:HOH4014 2.2 58.6 1.0
O A:HOH4012 2.2 59.5 1.0
OE2 B:GLU112 4.1 39.9 1.0
O A:HOH4153 4.1 56.6 1.0
OE2 A:GLU159 4.2 35.2 1.0
OE2 A:GLU151 4.3 48.3 1.0
OE1 B:GLU112 4.3 37.3 1.0
O B:HOH4228 4.4 61.4 1.0
O B:HOH4325 4.4 73.1 1.0
O A:HOH4137 4.5 53.4 1.0
CD B:GLU112 4.6 35.7 1.0
CG1 A:VAL158 4.9 28.6 1.0

Magnesium binding site 4 out of 12 in 2nv1

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Magnesium binding site 4 out of 12 in the Structure of the Synthase Subunit PDX1 (Yaad) of Plp Synthase From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the Synthase Subunit PDX1 (Yaad) of Plp Synthase From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3010

b:58.9
occ:1.00
 O B:HOH4019 2.2 56.3 1.0
O B:HOH4018 2.2 58.8 1.0
O B:HOH4020 2.2 54.5 1.0
O B:HOH4017 2.2 56.0 1.0
O B:HOH4021 2.2 57.9 1.0
O B:HOH4022 2.2 53.1 1.0
O B:HOH4104 4.1 43.4 1.0
O B:HOH4383 4.1 79.6 1.0
O B:HOH4334 4.2 74.1 1.0
O B:HOH4201 4.2 58.7 1.0
O B:VAL74 4.2 37.4 1.0
O B:HOH4298 4.2 69.4 1.0
O B:HOH4409 4.3 83.2 1.0
O B:ILE76 4.3 36.1 1.0
O B:MET71 4.3 39.0 1.0
OD2 B:ASP99 4.5 32.0 1.0
O B:SER75 4.6 42.6 1.0
O B:HOH4359 4.6 77.2 1.0
O B:HOH4401 4.7 81.6 1.0
C B:SER75 4.8 40.0 1.0
CA B:SER75 4.9 40.4 1.0

Magnesium binding site 5 out of 12 in 2nv1

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Magnesium binding site 5 out of 12 in the Structure of the Synthase Subunit PDX1 (Yaad) of Plp Synthase From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of the Synthase Subunit PDX1 (Yaad) of Plp Synthase From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3015

b:65.5
occ:1.00
 O C:HOH4027 2.2 63.7 1.0
O B:HOH4024 2.2 61.8 1.0
O C:HOH4028 2.2 64.1 1.0
O B:HOH4023 2.2 65.4 1.0
O C:HOH4029 2.2 65.4 1.0
O C:HOH4026 2.2 63.9 1.0
OE2 B:GLU159 4.2 38.1 1.0
O B:HOH4267 4.2 66.6 1.0
OE2 C:GLU112 4.3 41.3 1.0
OE1 C:GLU112 4.4 39.1 1.0
O C:HOH4158 4.6 51.7 1.0
OE2 B:GLU151 4.6 50.4 1.0
CD C:GLU112 4.8 40.5 1.0
O B:HOH4301 4.8 69.9 1.0
O B:HOH4168 5.0 53.6 1.0

Magnesium binding site 6 out of 12 in 2nv1

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Magnesium binding site 6 out of 12 in the Structure of the Synthase Subunit PDX1 (Yaad) of Plp Synthase From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of the Synthase Subunit PDX1 (Yaad) of Plp Synthase From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3016

b:65.4
occ:1.00
 O C:HOH4033 2.2 65.9 1.0
O C:HOH4034 2.2 63.8 1.0
O C:HOH4030 2.2 64.2 1.0
O C:HOH4032 2.2 63.1 1.0
O C:HOH4031 2.2 65.8 1.0
O C:HOH4035 2.2 67.3 1.0
O C:HOH4204 4.1 58.6 1.0
O C:HOH4126 4.2 45.2 1.0
O C:VAL74 4.2 40.3 1.0
O C:ILE76 4.3 38.1 1.0
O C:MET71 4.3 40.1 1.0
O C:HOH4264 4.3 66.8 1.0
OD2 C:ASP99 4.3 32.7 1.0
O C:HOH4221 4.4 60.4 1.0
O C:HOH4328 4.4 75.3 1.0
O C:HOH4298 4.5 70.1 1.0
O C:SER75 4.5 44.5 1.0
O C:HOH4346 4.7 78.0 1.0
C C:SER75 4.7 42.1 1.0
CA C:SER75 4.8 42.3 1.0
CG2 C:VAL78 5.0 33.5 1.0

Magnesium binding site 7 out of 12 in 2nv1

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Magnesium binding site 7 out of 12 in the Structure of the Synthase Subunit PDX1 (Yaad) of Plp Synthase From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of the Synthase Subunit PDX1 (Yaad) of Plp Synthase From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3022

b:61.7
occ:1.00
 O D:HOH4039 2.2 58.0 1.0
O C:HOH4038 2.2 57.8 1.0
O C:HOH4036 2.2 61.2 1.0
O C:HOH4037 2.2 57.5 1.0
O D:HOH4038 2.2 58.6 1.0
O D:HOH4040 2.2 58.6 1.0
OE2 D:GLU112 4.1 41.2 1.0
OE2 C:GLU159 4.2 38.2 1.0
OE1 D:GLU112 4.3 38.8 1.0
O C:HOH4180 4.3 55.4 1.0
O D:HOH4342 4.3 74.3 1.0
OE2 C:GLU151 4.4 47.8 1.0
O C:HOH4223 4.5 60.7 1.0
O C:HOH4293 4.6 69.3 1.0
CD D:GLU112 4.6 38.1 1.0
CG1 C:VAL158 4.9 31.9 1.0

Magnesium binding site 8 out of 12 in 2nv1

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Magnesium binding site 8 out of 12 in the Structure of the Synthase Subunit PDX1 (Yaad) of Plp Synthase From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of the Synthase Subunit PDX1 (Yaad) of Plp Synthase From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg3023

b:64.1
occ:1.00
 O D:HOH4044 2.2 62.4 1.0
O D:HOH4045 2.2 62.4 1.0
O D:HOH4041 2.2 62.4 1.0
O D:HOH4046 2.2 62.4 1.0
O D:HOH4042 2.2 62.2 1.0
O D:HOH4043 2.2 63.5 1.0
O D:VAL74 4.1 37.6 1.0
O D:MET71 4.2 39.7 1.0
O D:HOH4165 4.2 50.9 1.0
O D:ILE76 4.3 35.6 1.0
O D:HOH4311 4.4 70.6 1.0
O D:HOH4185 4.4 54.5 1.0
O D:HOH4322 4.4 72.1 1.0
OD2 D:ASP99 4.4 33.4 1.0
O D:HOH4124 4.5 44.1 1.0
O D:SER75 4.6 42.8 1.0
O D:HOH4402 4.6 85.6 1.0
O D:HOH4320 4.7 71.5 1.0
C D:SER75 4.8 40.1 1.0
CA D:SER75 4.9 40.4 1.0
O D:HOH4405 4.9 85.9 1.0

Magnesium binding site 9 out of 12 in 2nv1

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Magnesium binding site 9 out of 12 in the Structure of the Synthase Subunit PDX1 (Yaad) of Plp Synthase From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of the Synthase Subunit PDX1 (Yaad) of Plp Synthase From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg3027

b:66.1
occ:1.00
 O E:HOH4050 2.2 61.1 1.0
O E:HOH4049 2.2 63.7 1.0
O D:HOH4048 2.2 64.3 1.0
O D:HOH4047 2.2 61.2 1.0
O E:HOH4051 2.2 62.6 1.0
O E:HOH4052 2.2 64.2 1.0
O E:HOH4356 4.0 72.0 1.0
OE2 D:GLU159 4.2 40.7 1.0
O D:HOH4204 4.3 56.8 1.0
OE2 E:GLU112 4.3 40.3 1.0
OE1 E:GLU112 4.4 37.5 1.0
OE2 D:GLU151 4.5 49.3 1.0
CD E:GLU112 4.8 38.6 1.0
CG1 D:VAL158 4.9 30.7 1.0

Magnesium binding site 10 out of 12 in 2nv1

Go back to Magnesium Binding Sites List in 2nv1
Magnesium binding site 10 out of 12 in the Structure of the Synthase Subunit PDX1 (Yaad) of Plp Synthase From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structure of the Synthase Subunit PDX1 (Yaad) of Plp Synthase From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg3028

b:56.7
occ:1.00
 O E:HOH4058 2.2 58.3 1.0
O E:HOH4055 2.2 57.4 1.0
O E:HOH4054 2.2 57.3 1.0
O E:HOH4053 2.2 57.2 1.0
O E:HOH4057 2.2 57.7 1.0
O E:HOH4056 2.2 58.9 1.0
O E:HOH4121 4.1 40.3 1.0
O E:HOH4213 4.1 56.5 1.0
O E:HOH4321 4.1 67.4 1.0
O E:VAL74 4.2 41.0 1.0
O E:HOH4286 4.2 63.2 1.0
O E:MET71 4.2 38.5 1.0
O E:ILE76 4.3 36.6 1.0
O E:HOH4201 4.3 54.8 1.0
O E:HOH4398 4.4 77.5 1.0
OD2 E:ASP99 4.5 33.0 1.0
O E:HOH4285 4.5 63.1 1.0
O E:SER75 4.6 42.6 1.0
C E:SER75 4.8 40.1 1.0
CA E:SER75 4.8 40.8 1.0

Reference:

M.Strohmeier, T.Raschle, J.Mazurkiewicz, K.Rippe, I.Sinning, T.B.Fitzpatrick, I.Tews. Structure of A Bacterial Pyridoxal 5'-Phosphate Synthase Complex Proc.Natl.Acad.Sci.Usa V. 103 19284 2006.
ISSN: ISSN 0027-8424
PubMed: 17159152
DOI: 10.1073/PNAS.0604950103
Page generated: Mon Dec 14 07:31:08 2020

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