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

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

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

Magnesium

(Mg)

7 atoms

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

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of S25-2 Fab Unliganded 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn214 b:55.9 occ:1.00 OE2 A:GLU184 2.0 49.4 1.0 NE2 A:HIS188 2.2 44.0 1.0 OE1 A:GLU184 2.3 41.0 1.0 O A:HOH690 2.3 35.9 1.0 CD A:GLU184 2.4 45.3 1.0 O A:HOH702 2.5 50.4 1.0 CD2 A:HIS188 3.1 42.6 1.0 CE1 A:HIS188 3.2 42.2 1.0 CG A:GLU184 3.9 46.8 1.0 NH1 A:ARG187 4.0 59.1 1.0 NE A:ARG187 4.1 59.4 1.0 NH2 A:ARG154 4.2 62.0 1.0 ND1 A:HIS188 4.3 41.5 1.0 CG A:HIS188 4.3 40.8 1.0 CZ A:ARG187 4.5 61.0 1.0 CB A:ARG187 4.9 48.7 1.0 CB A:GLU184 4.9 43.0 1.0

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of S25-2 Fab Unliganded 2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn214 b:61.4 occ:1.00 NE2 C:HIS188 2.1 39.7 1.0 OE1 C:GLU184 2.2 37.9 1.0 O C:HOH688 2.5 56.9 1.0 OE2 C:GLU184 2.5 40.2 1.0 CD C:GLU184 2.7 39.6 1.0 O C:HOH674 3.0 44.7 1.0 CE1 C:HIS188 3.1 37.5 1.0 CD2 C:HIS188 3.2 36.7 1.0 NE C:ARG187 4.2 51.6 1.0 ND1 C:HIS188 4.2 38.0 1.0 CG C:GLU184 4.2 40.1 1.0 CG C:HIS188 4.3 37.7 1.0 NH1 C:ARG187 4.5 51.8 1.0 CZ C:ARG187 4.8 54.2 1.0 CB C:ARG187 4.8 43.9 1.0

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of S25-2 Fab Unliganded 2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn215 b:56.0 occ:1.00 N C:ASP1 2.1 44.3 1.0 OD1 C:ASP1 2.2 51.9 1.0 CG C:ASP1 2.3 51.0 1.0 OD2 C:ASP1 2.7 53.9 1.0 CB C:ASP1 3.1 46.5 1.0 CA C:ASP1 3.1 42.0 1.0 C C:ASP1 4.4 38.7 1.0 O C:ASP1 4.6 38.5 1.0

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