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Magnesium in PDB 4lzw: X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Thymidine at 1.29 A Resolution

Enzymatic activity of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Thymidine at 1.29 A Resolution

All present enzymatic activity of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Thymidine at 1.29 A Resolution:
2.4.2.3;

Protein crystallography data

The structure of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Thymidine at 1.29 A Resolution, PDB code: 4lzw was solved by I.I.Prokofev, A.A.Lashkov, A.G.Gabdoulkhakov, C.Betzel, A.M.Mikhailov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.89 / 1.29
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 91.740, 95.850, 91.830, 90.00, 119.96, 90.00
R / Rfree (%) 17.8 / 21

Other elements in 4lzw:

The structure of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Thymidine at 1.29 A Resolution also contains other interesting chemical elements:

Chlorine (Cl) 8 atoms
Sodium (Na) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Thymidine at 1.29 A Resolution (pdb code 4lzw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Thymidine at 1.29 A Resolution, PDB code: 4lzw:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 4lzw

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Magnesium binding site 1 out of 7 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Thymidine at 1.29 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Thymidine at 1.29 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg307

b:19.2
occ:0.54
 O A:HOH513 2.0 19.3 1.0
O A:HOH562 2.1 19.3 0.6
O C:HOH656 2.1 20.8 0.6
O A:HOH688 2.1 21.5 0.5
O A:HOH621 2.1 19.5 0.6
OE1 A:GLN180 2.1 16.4 0.7
OE1 A:GLN180 2.9 14.0 0.3
CD A:GLN180 3.0 13.7 0.7
NE2 A:GLN180 3.3 12.7 0.7
NE2 A:GLN180 3.3 12.3 0.3
CD A:GLN180 3.4 12.3 0.3
O A:HOH630 3.9 21.3 0.5
O C:HOH498 4.0 16.9 1.0
OE2 C:GLU185 4.1 13.8 1.0
O A:HOH562 4.2 13.8 0.4
O C:HOH503 4.3 19.0 1.0
CG A:GLN180 4.4 12.0 0.7
O C:HOH626 4.5 23.2 1.0
CG A:GLN180 4.7 10.6 0.3
CA A:ARG177 4.7 8.1 1.0
CB A:GLN180 4.8 10.2 0.7
CG A:ARG177 4.8 12.3 1.0
CB A:ARG177 4.8 10.3 1.0
CB A:GLN180 4.8 9.5 0.3
CD C:GLU185 5.0 12.9 1.0

Magnesium binding site 2 out of 7 in 4lzw

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Magnesium binding site 2 out of 7 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Thymidine at 1.29 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Thymidine at 1.29 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg305

b:15.5
occ:0.58
 O B:HOH503 2.0 17.8 1.0
O B:HOH524 2.0 18.8 1.0
O B:HOH559 2.1 15.2 0.6
OE1 B:GLN180 2.2 13.1 0.6
OE1 B:GLN180 2.5 9.7 0.4
O B:HOH454 2.9 27.4 0.7
O B:HOH454 2.9 21.2 0.3
CD B:GLN180 3.0 11.2 0.6
NE2 B:GLN180 3.0 10.8 0.6
CD B:GLN180 3.3 9.1 0.4
NE2 B:GLN180 3.5 9.3 0.4
O B:HOH689 3.9 35.7 1.0
O F:HOH474 4.1 14.6 1.0
O F:HOH643 4.1 37.5 1.0
OE1 F:GLU185 4.1 8.2 0.6
O B:HOH523 4.3 10.3 0.5
O F:HOH447 4.3 14.5 1.0
O B:HOH478 4.4 17.2 1.0
CG B:GLN180 4.4 9.2 0.6
O B:HOH626 4.5 36.5 1.0
O F:HOH561 4.5 24.8 1.0
O B:HOH637 4.6 33.0 1.0
CG B:GLN180 4.7 7.8 0.4
CA B:ARG177 4.7 7.7 1.0
CB B:ARG177 4.8 9.8 1.0
CG B:ARG177 4.9 11.7 1.0
CB B:GLN180 4.9 8.2 0.6
CD F:GLU185 5.0 7.2 0.6

Magnesium binding site 3 out of 7 in 4lzw

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Magnesium binding site 3 out of 7 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Thymidine at 1.29 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Thymidine at 1.29 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg305

b:17.3
occ:0.82
 O C:HOH486 2.0 17.6 1.0
O C:HOH660 2.0 20.6 1.0
O C:HOH561 2.0 19.9 1.0
O C:HOH492 2.1 19.2 1.0
MG C:MG306 3.0 17.9 0.4
O C:HOH514 3.9 23.4 1.0
O C:HOH628 4.0 26.2 1.0
OD1 C:ASN102 4.0 16.7 1.0
O C:PRO99 4.1 15.2 1.0
O C:HOH695 4.1 31.0 1.0
ND2 C:ASN102 4.6 15.8 1.0
CA C:HIS100 4.7 11.9 1.0
CG C:ASN102 4.7 14.9 1.0
O C:HOH488 4.8 17.6 1.0

Magnesium binding site 4 out of 7 in 4lzw

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Magnesium binding site 4 out of 7 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Thymidine at 1.29 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Thymidine at 1.29 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg306

b:17.9
occ:0.39
 OD1 C:ASN102 1.7 16.7 1.0
O C:HOH488 2.1 17.6 1.0
O C:HOH492 2.1 19.2 1.0
O C:HOH486 2.1 17.6 1.0
CG C:ASN102 2.7 14.9 1.0
MG C:MG305 3.0 17.3 0.8
ND2 C:ASN102 3.3 15.8 1.0
CB C:ASN102 4.0 11.9 1.0
O C:HOH474 4.2 16.7 1.0
O C:HOH628 4.2 26.2 1.0
O C:PRO99 4.2 15.2 1.0
O C:HOH660 4.4 20.6 1.0
NE2 C:GLN224 4.5 10.5 1.0
O C:HOH739 4.5 35.3 1.0
CA C:ASN102 4.5 9.9 1.0
O C:HOH561 4.6 19.9 1.0
O C:HOH695 4.7 31.0 1.0

Magnesium binding site 5 out of 7 in 4lzw

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Magnesium binding site 5 out of 7 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Thymidine at 1.29 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Thymidine at 1.29 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg304

b:15.5
occ:0.84
 O D:HOH528 2.0 17.1 1.0
O D:HOH568 2.0 18.0 1.0
O D:HOH470 2.0 16.3 1.0
MG D:MG305 2.9 15.4 0.5
O D:HOH612 3.9 30.0 1.0
O D:HOH621 4.1 25.3 1.0
OD1 D:ASN102 4.1 16.7 1.0
O D:PRO99 4.1 13.0 1.0
O D:HOH666 4.6 15.8 1.0
ND2 D:ASN102 4.6 16.3 1.0
CA D:HIS100 4.7 12.3 1.0
O D:HOH707 4.7 34.2 0.4
CG D:ASN102 4.8 15.4 1.0

Magnesium binding site 6 out of 7 in 4lzw

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Magnesium binding site 6 out of 7 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Thymidine at 1.29 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Thymidine at 1.29 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg305

b:15.4
occ:0.51
 OD1 D:ASN102 1.8 16.7 1.0
O D:HOH528 2.1 17.1 1.0
O D:HOH666 2.1 15.8 1.0
O D:HOH470 2.2 16.3 1.0
CG D:ASN102 2.7 15.4 1.0
MG D:MG304 2.9 15.5 0.8
ND2 D:ASN102 3.2 16.3 1.0
CB D:ASN102 4.0 12.2 1.0
O D:HOH495 4.1 12.9 1.0
O D:PRO99 4.2 13.0 1.0
O D:HOH621 4.3 25.3 1.0
O D:HOH568 4.4 18.0 1.0
NE2 D:GLN224 4.5 9.8 1.0
CA D:ASN102 4.5 9.6 1.0

Magnesium binding site 7 out of 7 in 4lzw

Go back to Magnesium Binding Sites List in 4lzw
Magnesium binding site 7 out of 7 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Thymidine at 1.29 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Thymidine at 1.29 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg305

b:18.9
occ:0.68
 NE2 E:GLN180 2.0 18.9 0.4
O E:HOH562 2.0 20.7 1.0
O E:HOH619 2.0 18.2 0.7
O E:HOH468 2.0 17.8 1.0
O E:HOH574 2.1 20.1 1.0
O E:HOH622 2.1 21.3 1.0
OE1 E:GLN180 2.4 18.4 0.4
OE1 E:GLN180 2.4 10.3 0.6
CD E:GLN180 2.5 17.6 0.4
CD E:GLN180 3.3 9.6 0.6
NE2 E:GLN180 3.7 10.7 0.6
O E:HOH603 4.0 29.9 1.0
CG E:GLN180 4.0 15.1 0.4
O E:HOH511 4.1 11.7 0.6
OE2 A:GLU185 4.1 9.4 0.6
O A:HOH465 4.2 13.8 1.0
O A:HOH458 4.3 14.8 1.0
O E:HOH503 4.4 18.8 1.0
OE2 A:GLU185 4.4 14.4 0.4
O A:HOH624 4.5 26.9 1.0
CG E:GLN180 4.6 8.3 0.6
CB E:GLN180 4.7 12.5 0.4
CA E:ARG177 4.7 8.1 1.0
CB E:ARG177 4.8 10.7 1.0
CB E:GLN180 4.9 8.2 0.6
CG E:ARG177 4.9 12.5 1.0
CD A:GLU185 4.9 8.2 0.6

Reference:

I.I.Prokofev, A.A.Lashkov, A.G.Gabdoulkhakov, C.Betzel, A.M.Mikhailov. X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with Thymidine at 1.29 A Resolution To Be Published.
Page generated: Mon Dec 14 19:11:08 2020

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