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Magnesium in PDB 1q9k: S25-2 Fab Unliganded 1

Protein crystallography data

The structure of S25-2 Fab Unliganded 1, PDB code: 1q9k 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) 19.74 / 1.96
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 96.800, 112.200, 41.500, 90.00, 90.00, 90.00
R / Rfree (%) 22.8 / 27.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the S25-2 Fab Unliganded 1 (pdb code 1q9k). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the S25-2 Fab Unliganded 1, PDB code: 1q9k:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 1q9k

Go back to Magnesium Binding Sites List in 1q9k
Magnesium binding site 1 out of 4 in the S25-2 Fab Unliganded 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of S25-2 Fab Unliganded 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg214

b:23.4
occ:1.00
N A:PHE97 3.1 28.0 1.0
O B:HOH331 3.1 43.0 1.0
N B:TRP47 3.2 28.8 1.0
O B:HOH429 3.2 49.2 1.0
CA A:THR96 3.6 31.6 1.0
CA B:GLU46 3.9 27.6 1.0
C A:THR96 3.9 30.4 1.0
CB B:TRP47 3.9 29.1 1.0
CD2 A:PHE97 4.0 27.6 1.0
OG1 A:THR96 4.0 38.2 1.0
C B:GLU46 4.0 27.3 1.0
CB A:PHE97 4.1 25.0 1.0
CA A:PHE97 4.1 27.6 1.0
CA B:TRP47 4.2 28.2 1.0
O B:LEU45 4.2 26.4 1.0
O A:PHE97 4.2 28.1 1.0
CB A:THR96 4.3 32.7 1.0
CG B:GLU46 4.4 33.0 1.0
O A:ARG95 4.5 30.6 1.0
O B:TRP47 4.5 27.9 1.0
CG A:PHE97 4.5 26.4 1.0
C A:PHE97 4.7 28.2 1.0
CB B:GLU46 4.7 29.4 1.0
N A:THR96 4.7 30.5 1.0
N B:GLU46 4.9 27.1 1.0
C B:TRP47 4.9 28.1 1.0
C B:LEU45 4.9 26.7 1.0

Magnesium binding site 2 out of 4 in 1q9k

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Magnesium binding site 2 out of 4 in the S25-2 Fab Unliganded 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of S25-2 Fab Unliganded 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg215

b:58.9
occ:1.00
NZ A:LYS168 2.0 30.9 1.0
CE A:LYS168 2.3 36.7 1.0
O A:HOH548 2.6 41.0 1.0
NE2 B:HIS162 3.3 42.7 1.0
ND2 A:ASN137 3.3 34.8 1.0
CE1 B:HIS162 3.4 42.2 1.0
CD A:LYS168 3.5 40.8 1.0
OD1 A:ASP166 3.6 44.4 1.0
OD1 A:ASN137 3.8 35.3 1.0
O A:HOH547 4.0 49.0 1.0
CG A:ASN137 4.0 34.5 1.0
CD2 B:HIS162 4.4 40.7 1.0
ND1 B:HIS162 4.5 40.8 1.0
CG A:ASP166 4.5 43.0 1.0
OD2 A:ASP166 4.6 43.3 1.0
OD1 A:ASP169 4.8 44.6 1.0
O B:HOH442 4.8 41.5 1.0
CG A:LYS168 4.9 43.4 1.0
O A:HOH323 5.0 25.6 1.0

Magnesium binding site 3 out of 4 in 1q9k

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Magnesium binding site 3 out of 4 in the S25-2 Fab Unliganded 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of S25-2 Fab Unliganded 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg216

b:45.1
occ:1.00
OG1 A:THR101 2.6 26.9 1.0
OE1 A:GLN6 2.7 30.9 1.0
O A:SER22 2.9 31.7 1.0
CB A:MET21 3.3 27.8 1.0
CB A:GLN6 3.4 30.2 1.0
CG A:GLN6 3.4 30.0 1.0
CD A:GLN6 3.4 28.4 1.0
CG A:MET21 3.6 31.2 1.0
O A:SER7 3.6 31.8 1.0
N A:SER22 3.6 29.4 1.0
C A:SER22 3.7 31.1 1.0
CB A:THR101 3.7 24.8 1.0
N A:SER7 3.8 30.7 1.0
CZ3 A:TRP35 3.8 26.9 1.0
CH2 A:TRP35 3.9 27.6 1.0
C A:MET21 4.0 28.1 1.0
CA A:GLN6 4.0 30.8 1.0
CA A:MET21 4.1 28.6 1.0
CA A:SER22 4.2 29.8 1.0
SD A:MET21 4.3 33.4 1.0
C A:SER7 4.3 30.8 1.0
C A:GLN6 4.3 31.1 1.0
CG2 A:THR101 4.6 27.4 1.0
N A:CYS23 4.6 32.0 1.0
O A:MET21 4.6 26.0 1.0
CA A:SER7 4.7 32.0 1.0
NE2 A:GLN6 4.7 24.8 1.0
N A:THR101 4.8 28.0 1.0
CA A:THR101 4.8 27.8 1.0
O A:PRO8 4.9 32.5 1.0
CB A:CYS23 4.9 33.5 1.0
CA A:CYS23 4.9 33.0 1.0

Magnesium binding site 4 out of 4 in 1q9k

Go back to Magnesium Binding Sites List in 1q9k
Magnesium binding site 4 out of 4 in the S25-2 Fab Unliganded 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of S25-2 Fab Unliganded 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg217

b:18.6
occ:1.00
O A:HOH404 1.9 36.9 1.0
NE2 A:HIS188 2.1 32.1 1.0
O A:HOH435 2.1 34.1 1.0
CE1 A:HIS188 3.0 31.9 1.0
CD2 A:HIS188 3.2 30.0 1.0
ND1 A:HIS188 4.2 31.4 1.0
CG A:HIS188 4.3 30.2 1.0
NE A:ARG187 4.3 38.3 1.0
O A:GLU184 4.7 31.6 1.0
NH1 A:ARG187 4.7 38.3 1.0
CB A:ARG187 4.8 32.7 1.0
NH2 A:ARG154 4.9 71.4 1.0
O A:HOH448 4.9 43.4 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 06:38:23 2020

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