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Magnesium in PDB 1q9l: S25-2 Fab Unliganded 2

Protein crystallography data

The structure of S25-2 Fab Unliganded 2, PDB code: 1q9l 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) 19.85 / 2.28
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.700, 96.000, 114.200, 90.00, 90.00, 90.00
R / Rfree (%) 21.6 / 28.6

Other elements in 1q9l:

The structure of S25-2 Fab Unliganded 2 also contains other interesting chemical elements:

Zinc (Zn) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the S25-2 Fab Unliganded 2 (pdb code 1q9l). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the S25-2 Fab Unliganded 2, PDB code: 1q9l:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 1q9l

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Magnesium binding site 1 out of 7 in the S25-2 Fab Unliganded 2


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg212

b:27.1
occ:1.00
 O B:HOH362 2.8 26.9 1.0
N A:PHE97 3.1 26.8 1.0
N B:TRP47 3.3 28.7 1.0
O B:HOH341 3.6 39.1 1.0
CA A:THR96 3.6 27.2 1.0
CA B:GLU46 3.8 29.2 1.0
C A:THR96 3.9 27.0 1.0
CD2 A:PHE97 3.9 27.9 1.0
OG1 A:THR96 3.9 30.3 1.0
CB A:THR96 3.9 26.4 1.0
CB B:TRP47 4.0 27.8 1.0
CB A:PHE97 4.0 25.4 1.0
CA A:PHE97 4.0 27.6 1.0
C B:GLU46 4.1 28.3 1.0
O A:PHE97 4.2 30.2 1.0
CA B:TRP47 4.2 28.6 1.0
O B:LEU45 4.4 25.2 1.0
CG A:PHE97 4.5 29.1 1.0
O B:TRP47 4.5 27.8 1.0
O A:ARG95 4.6 29.4 1.0
CB B:GLU46 4.6 29.2 1.0
C A:PHE97 4.6 28.0 1.0
CG B:GLU46 4.6 32.9 1.0
O B:HOH561 4.8 47.3 1.0
N A:THR96 4.8 28.1 1.0
N B:GLU46 4.8 26.6 1.0
C B:TRP47 4.9 28.4 1.0
C B:LEU45 5.0 25.7 1.0

Magnesium binding site 2 out of 7 in 1q9l

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Magnesium binding site 2 out of 7 in the S25-2 Fab Unliganded 2


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg212

b:24.6
occ:1.00
 OD2 D:ASP171 3.2 52.3 1.0
OD1 D:ASP171 3.2 50.4 1.0
CG D:ASP171 3.4 48.3 1.0
O D:HOH711 3.6 24.3 1.0
O D:SER170 4.0 45.0 1.0
C D:SER170 4.2 44.4 1.0
N D:ASP171 4.5 43.8 1.0
CB D:ASP171 4.6 44.7 1.0
CA D:ASP171 4.7 43.5 1.0
CA D:SER170 4.7 45.1 1.0

Magnesium binding site 3 out of 7 in 1q9l

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Magnesium binding site 3 out of 7 in the S25-2 Fab Unliganded 2


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg215

b:38.0
occ:1.00
 OD1 A:ASP166 1.9 47.7 1.0
O B:HOH303 2.4 43.6 1.0
O A:HOH694 2.4 30.1 1.0
O A:HOH701 2.6 48.2 1.0
CE1 B:HIS162 2.6 37.4 1.0
CG A:ASP166 2.8 44.6 1.0
O B:HOH695 2.8 31.3 1.0
NZ A:LYS168 3.0 53.1 1.0
OD2 A:ASP166 3.2 43.2 1.0
NE2 B:HIS162 3.4 37.1 1.0
ND1 B:HIS162 3.6 39.0 1.0
O B:HOH405 4.0 55.3 1.0
CB A:ASP166 4.1 43.4 1.0
O A:HOH355 4.3 39.4 1.0
CE A:LYS168 4.3 54.5 1.0
ND2 A:ASN137 4.4 39.0 1.0
CD2 B:HIS162 4.6 36.7 1.0
O A:HOH580 4.7 27.2 1.0
CG B:HIS162 4.7 36.6 1.0
OD2 A:ASP169 4.9 42.4 1.0

Magnesium binding site 4 out of 7 in 1q9l

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Magnesium binding site 4 out of 7 in the S25-2 Fab Unliganded 2


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg216

b:19.7
occ:1.00
 O D:HOH504 2.6 24.0 1.0
N C:PHE97 3.1 26.9 1.0
N D:TRP47 3.1 26.0 1.0
O D:HOH460 3.5 38.6 1.0
CA C:THR96 3.5 27.8 1.0
OG1 C:THR96 3.7 30.0 1.0
CA D:GLU46 3.8 25.3 1.0
CD2 C:PHE97 3.8 25.9 1.0
C C:THR96 3.8 27.8 1.0
CB C:THR96 3.8 27.5 1.0
CB D:TRP47 3.8 26.4 1.0
C D:GLU46 4.0 25.6 1.0
CA D:TRP47 4.1 26.5 1.0
CA C:PHE97 4.2 26.1 1.0
CB C:PHE97 4.2 26.9 1.0
O D:LEU45 4.3 23.9 1.0
O C:PHE97 4.3 26.5 1.0
CG C:PHE97 4.4 27.4 1.0
O C:ARG95 4.5 27.2 1.0
O C:HOH437 4.5 41.9 1.0
O D:TRP47 4.5 27.2 1.0
N C:THR96 4.6 27.6 1.0
CG D:GLU46 4.7 30.7 1.0
CB D:GLU46 4.7 26.1 1.0
C C:PHE97 4.7 25.9 1.0
N D:GLU46 4.7 24.7 1.0
CE2 C:PHE97 4.7 27.8 1.0
C D:TRP47 4.8 27.7 1.0
C D:LEU45 4.9 24.4 1.0
C C:ARG95 4.9 29.3 1.0

Magnesium binding site 5 out of 7 in 1q9l

Go back to Magnesium Binding Sites List in 1q9l
Magnesium binding site 5 out of 7 in the S25-2 Fab Unliganded 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of S25-2 Fab Unliganded 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg217

b:29.9
occ:1.00
 O C:HOH631 2.3 36.1 1.0
NZ C:LYS89 2.6 32.0 1.0
OD1 D:ASP95 2.6 58.6 1.0
CD C:ARG95 3.3 35.4 1.0
CG D:ASP95 3.5 59.8 1.0
NE C:ARG95 3.5 37.2 1.0
CG C:ARG95 3.5 35.4 1.0
CE C:LYS89 3.6 33.0 1.0
CD C:LYS89 3.8 30.7 1.0
OD2 D:ASP95 3.8 59.0 1.0
OG D:SER35 4.1 30.4 1.0
CB C:ARG95 4.2 32.5 1.0
CD1 D:TRP47 4.5 27.4 1.0
CB D:SER35 4.5 29.9 1.0
NE1 D:TRP47 4.6 29.4 1.0
CB D:ASP95 4.7 61.2 1.0
CZ C:ARG95 4.7 36.9 1.0
O C:HOH683 4.8 38.3 1.0
OH C:TYR36 4.8 35.1 1.0

Magnesium binding site 6 out of 7 in 1q9l

Go back to Magnesium Binding Sites List in 1q9l
Magnesium binding site 6 out of 7 in the S25-2 Fab Unliganded 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of S25-2 Fab Unliganded 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg218

b:37.3
occ:1.00
 OD1 C:ASP166 1.8 47.4 1.0
O C:HOH314 2.0 34.1 1.0
NZ C:LYS168 2.0 56.0 1.0
NE2 D:HIS162 2.2 41.1 1.0
O D:HOH351 2.7 33.9 1.0
CG C:ASP166 2.9 43.8 1.0
CD2 D:HIS162 3.0 40.7 1.0
CE1 D:HIS162 3.2 42.0 1.0
CE C:LYS168 3.3 57.6 1.0
OD2 C:ASP166 3.4 41.2 1.0
ND2 C:ASN137 3.9 46.2 1.0
CD C:LYS168 4.1 55.4 1.0
CB C:ASP166 4.2 42.6 1.0
CG D:HIS162 4.2 39.7 1.0
ND1 D:HIS162 4.3 41.3 1.0
O D:HOH452 4.6 48.2 1.0
CG C:LYS168 4.7 52.3 1.0
CG C:ASN137 4.8 43.3 1.0
OD2 C:ASP169 4.9 38.1 1.0
OD1 C:ASN137 4.9 47.2 1.0
O D:VAL161 4.9 35.0 1.0
O C:HOH574 4.9 48.9 1.0

Magnesium binding site 7 out of 7 in 1q9l

Go back to Magnesium Binding Sites List in 1q9l
Magnesium binding site 7 out of 7 in the S25-2 Fab Unliganded 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of S25-2 Fab Unliganded 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg219

b:29.0
occ:1.00
 OG C:SER190 3.0 34.9 1.0
N C:GLY151 3.2 47.3 1.0
OG1 C:THR192 3.3 33.4 1.0
O C:LYS148 3.3 40.2 1.0
N C:ASP150 3.4 42.4 1.0
CB C:SER190 3.5 34.2 1.0
O C:SER190 3.6 32.7 1.0
C C:SER190 3.7 32.1 1.0
C C:LYS148 3.8 40.3 1.0
CB C:THR192 3.8 31.5 1.0
CA C:ASP150 4.0 44.4 1.0
N C:THR192 4.0 30.5 1.0
N C:TYR191 4.0 32.0 1.0
C C:ILE149 4.0 40.7 1.0
C C:ASP150 4.1 46.4 1.0
CB C:LYS148 4.1 41.1 1.0
CA C:GLY151 4.1 49.8 1.0
N C:ILE149 4.2 38.5 1.0
CA C:SER190 4.2 32.3 1.0
CA C:ILE149 4.2 38.5 1.0
C C:TYR191 4.3 29.9 1.0
CA C:TYR191 4.4 29.9 1.0
CA C:THR192 4.6 31.9 1.0
CA C:LYS148 4.6 40.9 1.0
O C:ILE149 5.0 39.8 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 11:11:10 2024

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