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Magnesium in PDB 2p42: Complex of A Camelid Single-Domain Vhh Antibody Fragment with Rnase A at 1.8A Resolution: SE3-Mono-2 Crystal Form with Three Se-Met Sites (M34, M51, M83) in Vhh Scaffold

Enzymatic activity of Complex of A Camelid Single-Domain Vhh Antibody Fragment with Rnase A at 1.8A Resolution: SE3-Mono-2 Crystal Form with Three Se-Met Sites (M34, M51, M83) in Vhh Scaffold

All present enzymatic activity of Complex of A Camelid Single-Domain Vhh Antibody Fragment with Rnase A at 1.8A Resolution: SE3-Mono-2 Crystal Form with Three Se-Met Sites (M34, M51, M83) in Vhh Scaffold:
3.1.27.5;

Protein crystallography data

The structure of Complex of A Camelid Single-Domain Vhh Antibody Fragment with Rnase A at 1.8A Resolution: SE3-Mono-2 Crystal Form with Three Se-Met Sites (M34, M51, M83) in Vhh Scaffold, PDB code: 2p42 was solved by V.Tereshko, S.Uysal, A.Koide, K.Margalef, S.Koide, A.A.Kossiakoff, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 69.545, 55.002, 65.705, 90.00, 100.21, 90.00
R / Rfree (%) 17.1 / 21.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Complex of A Camelid Single-Domain Vhh Antibody Fragment with Rnase A at 1.8A Resolution: SE3-Mono-2 Crystal Form with Three Se-Met Sites (M34, M51, M83) in Vhh Scaffold (pdb code 2p42). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Complex of A Camelid Single-Domain Vhh Antibody Fragment with Rnase A at 1.8A Resolution: SE3-Mono-2 Crystal Form with Three Se-Met Sites (M34, M51, M83) in Vhh Scaffold, PDB code: 2p42:

Magnesium binding site 1 out of 1 in 2p42

Go back to Magnesium Binding Sites List in 2p42
Magnesium binding site 1 out of 1 in the Complex of A Camelid Single-Domain Vhh Antibody Fragment with Rnase A at 1.8A Resolution: SE3-Mono-2 Crystal Form with Three Se-Met Sites (M34, M51, M83) in Vhh Scaffold


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Complex of A Camelid Single-Domain Vhh Antibody Fragment with Rnase A at 1.8A Resolution: SE3-Mono-2 Crystal Form with Three Se-Met Sites (M34, M51, M83) in Vhh Scaffold within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg201

b:13.6
occ:1.00
 O C:HOH127 2.1 11.8 1.0
O C:HOH126 2.1 14.3 1.0
O A:HOH203 2.1 13.2 1.0
O A:HOH202 2.1 13.7 1.0
O C:HOH125 2.2 13.4 1.0
O A:HOH204 2.2 17.0 1.0
OE2 A:GLU49 4.1 18.1 1.0
OE2 C:GLU49 4.2 17.1 1.0
OE1 A:GLU49 4.2 20.4 1.0
OE1 C:GLU49 4.2 19.3 1.0
O C:HIS48 4.4 15.0 1.0
O A:SER18 4.5 19.4 1.0
O A:HOH261 4.5 29.7 1.0
O A:HIS48 4.5 17.2 1.0
CD A:GLU49 4.5 20.4 1.0
O C:HOH196 4.5 29.8 1.0
CD C:GLU49 4.5 18.4 1.0
CB C:SER18 4.5 19.4 1.0
O C:SER18 4.6 17.7 1.0
CB A:SER80 4.7 14.9 1.0
CB A:SER18 4.7 20.7 1.0
CB C:SER80 4.7 16.7 1.0
CA C:SER18 4.9 19.3 1.0
O A:HOH324 4.9 50.2 1.0
O C:HOH241 5.0 42.7 1.0
O A:HOH329 5.0 28.3 1.0
CA A:SER18 5.0 20.8 1.0

Reference:

V.Tereshko, S.Uysal, A.Koide, K.Margalef, S.Koide, A.A.Kossiakoff. Toward Chaperone-Assisted Crystallography: Protein Engineering Enhancement of Crystal Packing and X-Ray Phasing Capabilities of A Camelid Single-Domain Antibody (Vhh) Scaffold Protein Sci. V. 17 1175 2008.
ISSN: ISSN 0961-8368
PubMed: 18445622
DOI: 10.1110/PS.034892.108
Page generated: Wed Aug 14 02:03:18 2024

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