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Magnesium in PDB 1q9w: S45-18 Fab Pentasaccharide Bisphosphate Complex

Protein crystallography data

The structure of S45-18 Fab Pentasaccharide Bisphosphate Complex, PDB code: 1q9w was solved by H.P.Nguyen, N.O.Seto, C.R.Mackenzie, L.Brade, P.Kosma, H.Brade, S.V.Evans, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.90 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 71.200, 113.900, 133.900, 90.00, 90.00, 90.00
R / Rfree (%) 21.2 / 24.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the S45-18 Fab Pentasaccharide Bisphosphate Complex (pdb code 1q9w). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the S45-18 Fab Pentasaccharide Bisphosphate Complex, PDB code: 1q9w:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 1q9w

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Magnesium binding site 1 out of 5 in the S45-18 Fab Pentasaccharide Bisphosphate Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of S45-18 Fab Pentasaccharide Bisphosphate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg214

b:16.9
occ:1.00
 O B:HOH312 2.9 20.2 1.0
N A:PHE97 3.1 16.8 1.0
N B:TRP47 3.2 17.2 1.0
O B:HOH431 3.5 33.0 1.0
CA B:GLU46 3.6 17.5 1.0
CA A:THR96 3.7 16.2 1.0
CG2 A:THR96 3.9 20.4 1.0
CD2 A:PHE97 3.9 17.8 1.0
C B:GLU46 3.9 18.2 1.0
C A:THR96 3.9 16.0 1.0
CB A:PHE97 3.9 17.7 1.0
O B:HOH434 4.0 31.6 1.0
CA A:PHE97 4.0 17.9 1.0
CG B:GLU46 4.1 18.2 1.0
O B:LEU45 4.1 17.6 1.0
CB B:TRP47 4.1 18.0 1.0
O A:PHE97 4.2 16.8 1.0
CA B:TRP47 4.2 18.6 1.0
O B:HOH322 4.3 22.2 1.0
CB B:GLU46 4.3 16.7 1.0
CG A:PHE97 4.4 15.9 1.0
CB A:THR96 4.4 18.7 1.0
O B:TRP47 4.4 18.1 1.0
O A:HOH255 4.5 25.6 1.0
O A:ARG95 4.6 16.3 1.0
C A:PHE97 4.6 17.2 1.0
N B:GLU46 4.6 14.7 1.0
N A:THR96 4.8 15.5 1.0
C B:LEU45 4.8 17.4 1.0
C B:TRP47 4.8 17.9 1.0
CE2 A:PHE97 5.0 16.6 1.0

Magnesium binding site 2 out of 5 in 1q9w

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Magnesium binding site 2 out of 5 in the S45-18 Fab Pentasaccharide Bisphosphate Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of S45-18 Fab Pentasaccharide Bisphosphate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg215

b:26.0
occ:1.00
 OG1 A:THR101 2.8 17.3 1.0
O A:SER22 2.8 19.0 1.0
NE2 A:GLN6 2.9 14.6 1.0
CB A:GLN6 3.4 17.9 1.0
CB A:MET21 3.4 21.6 1.0
CG A:MET21 3.5 20.7 1.0
N A:SER22 3.6 15.9 1.0
CB A:THR101 3.6 16.7 1.0
C A:SER22 3.6 15.9 1.0
CG A:GLN6 3.6 16.3 1.0
CZ3 A:TRP35 3.7 20.9 1.0
CH2 A:TRP35 3.7 19.9 1.0
CD A:GLN6 3.7 15.4 1.0
SD A:MET21 3.8 24.4 1.0
C A:MET21 3.9 21.1 1.0
CA A:SER22 4.1 16.8 1.0
N A:PHE7 4.2 15.8 1.0
CA A:MET21 4.2 20.9 1.0
O A:PHE7 4.3 17.6 1.0
CA A:GLN6 4.3 16.8 1.0
CG2 A:THR101 4.5 17.3 1.0
O A:MET21 4.5 21.1 1.0
N A:CYS23 4.6 17.0 1.0
C A:GLN6 4.7 18.2 1.0
CA A:THR101 4.7 16.5 1.0
N A:THR101 4.7 17.6 1.0
C A:PHE7 4.8 16.5 1.0
O A:TYR86 4.8 19.1 1.0
OE1 A:GLN6 4.9 18.7 1.0
CE3 A:TRP35 5.0 19.0 1.0
CA A:CYS23 5.0 16.9 1.0

Magnesium binding site 3 out of 5 in 1q9w

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Magnesium binding site 3 out of 5 in the S45-18 Fab Pentasaccharide Bisphosphate Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of S45-18 Fab Pentasaccharide Bisphosphate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg306

b:23.1
occ:1.00
 O B:HOH379 2.0 24.3 1.0
O B:HOH376 2.0 24.2 1.0
O B:HOH378 2.1 25.0 1.0
O B:HOH377 2.1 22.3 1.0
OE2 B:GLU56 2.1 22.1 1.0
CD B:GLU56 3.2 24.1 1.0
OE1 B:GLU56 3.5 22.6 1.0
O B:THR55 4.0 19.7 1.0
NH1 B:ARG52 4.2 20.7 1.0
O B:HOH490 4.3 33.6 1.0
CG B:GLU56 4.4 20.2 1.0
CB B:THR54 4.7 19.9 1.0

Magnesium binding site 4 out of 5 in 1q9w

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Magnesium binding site 4 out of 5 in the S45-18 Fab Pentasaccharide Bisphosphate Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of S45-18 Fab Pentasaccharide Bisphosphate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg314

b:24.7
occ:1.00
 O C:HOH397 2.7 38.4 1.0
O D:HOH344 2.7 32.8 1.0
N C:PHE97 3.1 22.3 1.0
N D:TRP47 3.1 18.5 1.0
CA D:GLU46 3.6 18.2 1.0
CA C:THR96 3.7 23.5 1.0
C C:THR96 3.9 22.7 1.0
C D:GLU46 3.9 19.9 1.0
CG2 C:THR96 3.9 27.0 1.0
CD2 C:PHE97 4.0 20.5 1.0
CB D:TRP47 4.0 20.3 1.0
CB C:PHE97 4.0 22.2 1.0
CA C:PHE97 4.0 21.6 1.0
CG D:GLU46 4.1 22.2 1.0
O C:PHE97 4.1 22.3 1.0
CA D:TRP47 4.1 19.5 1.0
O D:HOH384 4.2 36.1 1.0
O D:LEU45 4.2 19.1 1.0
O C:HOH443 4.2 35.5 1.0
CB D:GLU46 4.4 19.8 1.0
CB C:THR96 4.4 23.9 1.0
O D:TRP47 4.4 21.9 1.0
CG C:PHE97 4.5 19.8 1.0
O C:ARG95 4.5 22.0 1.0
C C:PHE97 4.6 21.9 1.0
N D:GLU46 4.7 19.4 1.0
N C:THR96 4.7 23.3 1.0
C D:TRP47 4.8 21.2 1.0
C D:LEU45 4.9 20.1 1.0

Magnesium binding site 5 out of 5 in 1q9w

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Magnesium binding site 5 out of 5 in the S45-18 Fab Pentasaccharide Bisphosphate Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of S45-18 Fab Pentasaccharide Bisphosphate Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg315

b:32.5
occ:1.00
 OG1 C:THR101 2.7 21.2 1.0
NE2 C:GLN6 2.9 21.2 1.0
O C:SER22 2.9 24.2 1.0
CB C:MET21 3.5 24.4 1.0
CB C:GLN6 3.5 25.6 1.0
CG C:MET21 3.6 24.7 1.0
CB C:THR101 3.6 22.4 1.0
CG C:GLN6 3.7 24.2 1.0
C C:SER22 3.7 25.9 1.0
N C:SER22 3.7 24.5 1.0
CD C:GLN6 3.7 24.2 1.0
CZ3 C:TRP35 3.8 24.3 1.0
CH2 C:TRP35 3.9 23.4 1.0
SD C:MET21 3.9 27.1 1.0
C C:MET21 4.0 25.0 1.0
O C:PHE7 4.0 25.6 1.0
N C:PHE7 4.1 25.9 1.0
CA C:SER22 4.3 26.7 1.0
CA C:GLN6 4.3 26.9 1.0
CA C:MET21 4.3 25.7 1.0
O C:MET21 4.5 24.0 1.0
CG2 C:THR101 4.5 22.7 1.0
C C:PHE7 4.6 25.7 1.0
C C:GLN6 4.6 26.8 1.0
N C:CYS23 4.6 25.7 1.0
CA C:THR101 4.8 22.0 1.0
N C:THR101 4.8 22.8 1.0
O C:TYR86 4.8 20.7 1.0
CB C:CYS23 4.9 26.5 1.0
OE1 C:GLN6 4.9 23.4 1.0
CA C:CYS23 4.9 26.7 1.0
O C:PRO8 5.0 24.0 1.0
CA C:PHE7 5.0 26.9 1.0

Reference:

H.P.Nguyen, N.O.Seto, C.R.Mackenzie, L.Brade, P.Kosma, H.Brade, S.V.Evans. Germline Antibody Recognition of Distinct Carbohydrate Epitopes. Nat.Struct.Biol. V. 10 1019 2003.
ISSN: ISSN 1072-8368
PubMed: 14625588
DOI: 10.1038/NSB1014
Page generated: Mon Dec 14 06:38:29 2020

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