Atomistry » Magnesium » PDB 1q3b-1qc1 » 1q9l
Atomistry »
  Magnesium »
    PDB 1q3b-1qc1 »
      1q9l »

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

Go back to Magnesium Binding Sites List in 1q9l
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

Go back to Magnesium Binding Sites List in 1q9l
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

Go back to Magnesium Binding Sites List in 1q9l
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

Go back to Magnesium Binding Sites List in 1q9l
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: Sun Aug 10 02:59:07 2025

Last articles

Mg in 6LU1
Mg in 6LT4
Mg in 6LY7
Mg in 6LY6
Mg in 6LY3
Mg in 6LX1
Mg in 6LTW
Mg in 6LVW
Mg in 6LUH
Mg in 6LTS
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy