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Magnesium in PDB 1q9o: S45-18 Fab Unliganded

Protein crystallography data

The structure of S45-18 Fab Unliganded, PDB code: 1q9o 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) 19.18 / 1.79
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 76.400, 170.300, 77.100, 90.00, 114.40, 90.00
R / Rfree (%) 22 / 24.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the S45-18 Fab Unliganded (pdb code 1q9o). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the S45-18 Fab Unliganded, PDB code: 1q9o:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 1q9o

Go back to Magnesium Binding Sites List in 1q9o
Magnesium binding site 1 out of 4 in the S45-18 Fab Unliganded


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 Unliganded within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg214

b:24.4
occ:1.00
 O B:HOH437 2.5 28.6 1.0
N A:PHE97 2.9 18.8 1.0
O B:HOH446 2.9 19.1 1.0
N B:TRP47 3.0 17.7 1.0
CA A:THR96 3.6 19.6 1.0
CA B:GLU46 3.7 17.7 1.0
CD2 A:PHE97 3.7 20.1 1.0
CB A:PHE97 3.7 18.0 1.0
C A:THR96 3.7 20.0 1.0
CG2 A:THR96 3.8 21.2 1.0
C B:GLU46 3.8 18.2 1.0
CA A:PHE97 3.8 17.3 1.0
CB B:TRP47 3.8 18.8 1.0
CA B:TRP47 4.0 18.0 1.0
O B:LEU45 4.0 19.2 1.0
O A:PHE97 4.1 17.8 1.0
CG A:PHE97 4.2 16.7 1.0
O B:HOH543 4.2 31.3 1.0
CB A:THR96 4.3 19.1 1.0
CG B:GLU46 4.3 20.2 1.0
O B:HOH515 4.4 24.2 1.0
O B:TRP47 4.4 18.7 1.0
C A:PHE97 4.4 18.9 1.0
O B:HOH540 4.5 20.8 1.0
CB B:GLU46 4.5 18.7 1.0
O A:ARG95 4.6 20.3 1.0
O A:HOH510 4.6 33.5 1.0
N B:GLU46 4.6 17.9 1.0
N A:THR96 4.7 17.6 1.0
C B:LEU45 4.7 20.2 1.0
C B:TRP47 4.7 18.3 1.0
CE2 A:PHE97 4.8 19.6 1.0
O A:THR96 4.9 20.6 1.0

Magnesium binding site 2 out of 4 in 1q9o

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Magnesium binding site 2 out of 4 in the S45-18 Fab Unliganded


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 Unliganded within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg214

b:27.1
occ:1.00
 O D:HOH503 2.7 23.0 1.0
O C:HOH465 2.8 28.1 1.0
N C:PHE97 3.0 19.9 1.0
N D:TRP47 3.0 18.6 1.0
CA D:GLU46 3.6 18.9 1.0
CA C:THR96 3.6 21.0 1.0
CD2 C:PHE97 3.8 21.6 1.0
CB C:PHE97 3.8 18.1 1.0
C C:THR96 3.8 21.4 1.0
C D:GLU46 3.8 20.1 1.0
CB D:TRP47 3.8 18.8 1.0
CA C:PHE97 3.9 19.4 1.0
CG2 C:THR96 3.9 21.2 1.0
CA D:TRP47 4.0 18.6 1.0
CG D:GLU46 4.1 22.3 1.0
O C:HOH552 4.2 27.9 1.0
O C:PHE97 4.2 19.3 1.0
CG C:PHE97 4.2 20.6 1.0
O D:TRP47 4.3 18.7 1.0
O D:LEU45 4.3 19.9 1.0
CB D:GLU46 4.4 21.3 1.0
CB C:THR96 4.4 22.8 1.0
O D:HOH606 4.5 20.1 1.0
C C:PHE97 4.5 20.9 1.0
O C:ARG95 4.5 23.5 1.0
C D:TRP47 4.6 19.2 1.0
O C:HOH460 4.7 27.7 1.0
N C:THR96 4.7 22.4 1.0
N D:GLU46 4.7 19.9 1.0
O C:HOH835 4.8 29.0 1.0
CE2 C:PHE97 4.9 20.9 1.0
C D:LEU45 4.9 21.1 1.0
C C:ARG95 5.0 22.9 1.0
O C:THR96 5.0 21.0 1.0

Magnesium binding site 3 out of 4 in 1q9o

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Magnesium binding site 3 out of 4 in the S45-18 Fab Unliganded


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 Unliganded within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg214

b:26.0
occ:1.00
 OG1 A:THR101 2.7 23.1 1.0
O A:SER22 2.8 25.4 1.0
NE2 A:GLN6 2.8 18.8 1.0
CB A:THR101 3.4 22.7 1.0
CB A:MET21 3.4 27.8 1.0
N A:SER22 3.5 23.7 1.0
CG A:GLN6 3.6 19.7 1.0
O A:HOH309 3.6 27.9 1.0
C A:SER22 3.6 21.9 1.0
CB A:GLN6 3.7 21.2 1.0
CD A:GLN6 3.7 18.6 1.0
CZ3 A:TRP35 3.7 18.1 1.0
CH2 A:TRP35 3.8 17.0 1.0
C A:MET21 3.9 25.3 1.0
CA A:MET21 4.1 27.2 1.0
CA A:SER22 4.1 22.8 1.0
CG2 A:THR101 4.3 23.4 1.0
CA A:GLN6 4.4 21.4 1.0
CG A:MET21 4.4 27.7 1.0
O A:MET21 4.5 25.2 1.0
N A:THR101 4.6 20.4 1.0
CA A:THR101 4.6 24.3 1.0
N A:CYS23 4.6 22.7 1.0
O A:TYR86 4.7 21.7 1.0
C A:GLN6 4.8 22.8 1.0
SD A:MET21 4.8 28.4 1.0
OE1 A:GLN6 4.9 20.2 1.0
O A:PRO8 4.9 28.7 1.0
CE3 A:TRP35 5.0 17.1 1.0

Magnesium binding site 4 out of 4 in 1q9o

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Magnesium binding site 4 out of 4 in the S45-18 Fab Unliganded


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 Unliganded within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg214

b:33.1
occ:1.00
 NE2 C:GLN6 2.8 21.1 1.0
OG1 C:THR101 2.8 22.1 1.0
O C:SER22 3.0 25.9 1.0
CB C:MET21 3.4 27.6 1.0
CB C:THR101 3.5 21.4 1.0
CB C:GLN6 3.6 25.9 1.0
CD C:GLN6 3.7 24.5 1.0
N C:SER22 3.7 25.2 1.0
CG C:GLN6 3.7 22.4 1.0
CZ3 C:TRP35 3.7 20.8 1.0
C C:SER22 3.8 24.6 1.0
CH2 C:TRP35 3.8 21.0 1.0
C C:MET21 4.0 25.4 1.0
CA C:MET21 4.1 26.2 1.0
O C:PHE7 4.2 32.5 1.0
N C:PHE7 4.3 31.8 1.0
CG C:MET21 4.3 31.6 1.0
CA C:SER22 4.3 25.5 1.0
CA C:GLN6 4.4 28.1 1.0
CG2 C:THR101 4.4 20.1 1.0
O C:MET21 4.6 24.7 1.0
SD C:MET21 4.6 37.0 1.0
O C:TYR86 4.7 21.6 1.0
C C:GLN6 4.7 30.4 1.0
N C:CYS23 4.7 25.4 1.0
N C:THR101 4.7 20.7 1.0
C C:PHE7 4.7 32.8 1.0
CA C:THR101 4.7 21.4 1.0
OE1 C:GLN6 4.8 23.2 1.0
CE3 C:TRP35 5.0 19.5 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: Tue Aug 13 11:11:42 2024

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